ENT MERFISH Report

1. Overview

1.1 Sample Information

A brief sample information is generated from the submission table for the following analysis.

Sample Index and Basic Information
Expt Sample Index Case_Number Sex Age HPV Sample_Region Genotype Group Region DataPath Clinic.comment
1 NT28530x2 NT28530 1 M 52 Negative Left posterior BOT NT Normal region_NT28530x2 Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K.
1 TT28519x1 TT28519 1 M 52 Negative Left posterior BOT TT Tumor region_TT28519x1 Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K.
1 TT28519x2 TT28519_dup 1 M 52 Negative Left posterior BOT TT Tumor region_TT28519x2 Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K.
1 NT28530x1 NT28530_dup 1 M 52 Negative Left posterior BOT NT Normal region_NT28530x1 Y:_Imaging_data_2\202409271426_20240927ENT28519ImmunOnc500VA067x01_VMSC00101_234 Left posterior and BOT SCC. 15x years ago treated with chemorad for left tonsil K.

1.2 MERSCOPE Data Quality Summary

The summaries present the data quality assessment automatically generated by MERSCOPE for each experiment. We mainly focus on the transcripts level for each sample. So we’re looking for high density in transcripts, based on the transcripts count per field of view (FOV), transcript density in FOV, and frequency of transcripts detected.

Generally, log10 transcript count > 4.0 in most area can be considered as a good quality standard for human tissue.

Need to note that the low accuracy in DAPI cell boundary is not a concern, as a self-designed cell segmentation processing will take over this task.

1.2.1 NT28530x2(Normal)

1.2.2 TT28519x1(Tumor)

1.2.3 TT28519x2(Tumor)

1.2.4 NT28530x1(Normal)

1.3 Transcript Mis-Match on FOV Boundary

Due to issues with the Vizgen software, transcript alignment is incorrect during decoding, leading to misalignment problems at the field of view (FOV) boundary.

Vizgen has solved this issue by temporarily updating the decoding software to an unpublished beta version.

However, this update also made the “vzg” file being upgraded to “vzg2”. Current Vizgen Visualizer cannot recognize the new data format, which made Visualizer unusable for this dataset.

1.4 Autofluorescent issue

Autofluorescence is a major problem limiting the sensitivity of the detection of the fluorescence specifically derived from the applied dye or probe. As we can find it on DAPI imaging, there are many over-bright region.

Autofluorescence may occur due to the incomplete clearance of the tissue. Because of the presence of autofluorescence, the decoding would be confounded and the results in these cells would be artifacts.

As Dr. Tan highly recommends, we removed the portion of cell with autofluorescent issue, for better accuracy.

NT28530_DAPI_Imaging

NT28530_DAPI_Imaging

NT28530_DAPI_Imaging_small

NT28530_DAPI_Imaging_small

NT28530_dup_DAPI_Imaging

NT28530_dup_DAPI_Imaging

NT28530_dup_DAPI_Imaging_small

NT28530_dup_DAPI_Imaging_small

1.5 DAPI Imaging with Tumor-Associated Genes

Tumor_DAPI_Imaging

Tumor_DAPI_Imaging

Tumor_DAPI_Imaging

Tumor_DAPI_Imaging

Tumor_DAPI_Imaging

Tumor_DAPI_Imaging

2. Data Processing & Analysis

2.1 Cell Segmentation & Filtering

Based on the spatial information and images obtained from MERFISH, we developed a machine learning model using the Cellpose algorithm to distinguish individual cells via MERFISH DAPI images.

To ensure the data quality and accuracy of cells, we have defined the minimum and maximum values for cell volume and gene count per cell. The cell volume should be between [100, 2000], and the gene count per cell > 25.

After that, we successfully obtained high-quality and accurate cell and gene data. We are now ready to perform statistical analysis.

For analysis platform, all of the analysis and visualization are performed using Scanpy, a commonly used Python package toolkit for analyzing single-cell gene expression data.

2.1.2 Transcript Count Violin

The transcript level is a basic aspect of data quality control. After filtering, we have ensured that the minimum transcript count per cell > 25.

Transcript Count Violin After Filtering

Transcript Count Violin After Filtering

2.2 Batch Effect & Dimension Reduction

We conducted Leiden UMAP clustering, a non-linear, manifold-aware dimension reduction algorithm, on our dataset to subset the cells into clusters. The following annotations are based on the umap clustering.

Umap of cells and colored by batch

Umap of cells and colored by batch

3.Cell Annotation

To annotate individual cell types, we found the marker genes from database CellMarker.

We utilize FCRL5 and MZB1 for the identification of B cells, CCND1 and NOTCH1 for cancer cells, CD83 for dendritic cells, PLVAP and PDK4 for endothelial cells, and COL1A1 for fibroblasts. For macrophages, we apply CD14 in conjunction with CD163, while KIT is employed for mast cells, and TRAC, GATA3, and CD5 are used for T cells.

It is good to note that, so far what we have is a preliminary annotation, and we can potentially achieve further resolution on some cell types. For instance, T cells can be subdivided into regulatory T cells, helper T cells, natural killer T cells, and so on. However, the current sample size is insufficient for these detailed classifications. Once we have enough samples, further annotation should be feasible.

3.1 Markers for type annotation

3.2 Cell Type Umap

3.3 Cell Type Umap (group)

3.4 Cell Type Spatial Map

With the annotations, we can map cell types back to their physical positions and create a spatial map for each sample.

3.5 Cancer & T cell & B cell Spatial Map

3.6 Cell Type Qualification Analysis

Cell Type Count
cell_type_2 NT28530 NT28530_dup TT28519 TT28519_dup Total
B cell 2 3 1230 1031 2266
Cancer cell 34 30 465 362 891
Dendritic 2 0 133 110 245
Endothelial 1609 1427 1722 1341 6099
Fibroblast 2059 1732 19739 18582 42112
Macrophage 308 270 1915 1732 4225
Mast cell 35 33 474 486 1028
Smooth muscle cell 374 285 1644 1367 3670
T cell 115 82 811 676 1684
Total 4538 3862 28133 25687 62220

3.7 Cell Type Proportion Analysis

Based on the quantification of individual cell types, we are capable to compare the differences in cell numbers between various samples and genotypes. The proportion of each cell type is calculated by dividing the count of that specific cell type by the total cell count. The results are then visualized in a bar plot.

Notably, B cells, mast cells, and T cells show an obvious increase in tumor samples.

4. Gene differentiation (Tumor sample v.s. Normal sample)

Here, we use Wilcoxon rank-sum test to compute gene differential expression (DE). P value are adjusted using Benjamini–Hochberg procedure. The statistical significance was cut-off by log2(Fold Change) > 2 or log2(Fold Change) < -2 and p_value < 0.05.

The result are visualized via Volcano plot: a type of scatterplot that shows statistical significance (P value) versus magnitude of change (fold change).

The comparison is between Tumor and Normal samples. A positive fold change means higher expression in the tumor group.

4.0 Volcano plot to use

4.1 all

names scores logfoldchanges pvals pvals_adj
COL1A1 128.719830 85.216440 0.0000000 0.0000000
FN1 81.286490 7.571341 0.0000000 0.0000000
FOS -46.969980 -6.759444 0.0000000 0.0000000
PDK4 -60.815765 -6.633553 0.0000000 0.0000000
COL5A1 80.329340 6.229767 0.0000000 0.0000000
EGR1 -34.539925 -5.055663 0.0000000 0.0000000
VEGFA -39.941800 -5.038070 0.0000000 0.0000000
CD79A 5.999517 4.959108 0.0000000 0.0000000
JUN -66.503334 -4.828621 0.0000000 0.0000000
GPX3 -34.578636 -3.987802 0.0000000 0.0000000
MZB1 6.797644 3.979829 0.0000000 0.0000000
SERPINA1 11.236790 3.931262 0.0000000 0.0000000
FCRL5 4.486988 3.772412 0.0000072 0.0000276
CX3CL1 -8.829576 -3.658773 0.0000000 0.0000000
POU2AF1 17.934225 3.616645 0.0000000 0.0000000
FAP 6.151611 3.492644 0.0000000 0.0000000
TNC 32.630886 3.387915 0.0000000 0.0000000
DES -31.869339 -3.284775 0.0000000 0.0000000
TNF 9.065383 3.131130 0.0000000 0.0000000
MYH11 -5.373700 -3.080815 0.0000001 0.0000004
DUSP1 -52.305590 -3.073642 0.0000000 0.0000000
XBP1 6.826031 3.048380 0.0000000 0.0000000
MMP9 11.337405 3.016693 0.0000000 0.0000000
RORC -14.309868 -2.970993 0.0000000 0.0000000
MMP11 14.401033 2.840110 0.0000000 0.0000000
BMP1 54.718426 2.823937 0.0000000 0.0000000
COL11A1 25.157415 2.791966 0.0000000 0.0000000
CCR2 5.268528 2.779894 0.0000001 0.0000006
CR2 4.689729 2.658455 0.0000027 0.0000109
TP63 -4.827339 -2.616780 0.0000014 0.0000057
CXCL1 6.437659 2.539849 0.0000000 0.0000000
PPARGC1A -4.273971 -2.511725 0.0000192 0.0000717
JUNB -35.787884 -2.490444 0.0000000 0.0000000
DERL3 3.310865 2.451468 0.0009301 0.0028356
ITGAX 5.390393 2.434840 0.0000001 0.0000003
LGR6 -2.549464 -2.431690 0.0107889 0.0275226
LGR5 -5.406462 -2.327275 0.0000001 0.0000003
MUC1 9.941775 2.272612 0.0000000 0.0000000
HGF 4.867999 2.261392 0.0000011 0.0000047
CD19 2.838978 2.259758 0.0045258 0.0125717
IRF4 3.012619 2.251352 0.0025900 0.0075292
FLI1 5.158706 2.239080 0.0000002 0.0000011
NCAM1 -16.123442 -2.227492 0.0000000 0.0000000
CLCA1 3.899802 2.198663 0.0000963 0.0003366
PIK3CG 6.211835 2.155691 0.0000000 0.0000000
CD248 30.015327 2.120976 0.0000000 0.0000000
ESCO2 2.790225 2.114788 0.0052671 0.0143129
TNFRSF13C 2.781648 2.100781 0.0054084 0.0145386
CD27 2.849136 2.088706 0.0043838 0.0122453
LOX 4.607403 2.082753 0.0000041 0.0000161
CHEK2 7.125153 2.082282 0.0000000 0.0000000
TNFRSF9 3.862387 2.075009 0.0001123 0.0003845
SPRY2 -21.701843 -2.025791 0.0000000 0.0000000
SH2D1B -3.089103 -2.014404 0.0020076 0.0058702
IL6R -19.968603 -2.006788 0.0000000 0.0000000
NFKBIA -47.331722 -1.999478 0.0000000 0.0000000
PLA2G2A -5.787324 -1.949637 0.0000000 0.0000000
SOD2 -20.651323 -1.933330 0.0000000 0.0000000
EGFR -25.465170 -1.899327 0.0000000 0.0000000
EPHB3 9.868395 1.884270 0.0000000 0.0000000
ITGA4 3.441626 1.869566 0.0005782 0.0017957
CD1C 3.336021 1.854353 0.0008499 0.0026230
CCL5 4.015129 1.846842 0.0000594 0.0002153
MMP2 15.602754 1.844142 0.0000000 0.0000000
KLF2 -21.695911 -1.835344 0.0000000 0.0000000
PCNA 5.004646 1.832171 0.0000006 0.0000024
IRS1 26.424162 1.811546 0.0000000 0.0000000
CD276 20.552460 1.769813 0.0000000 0.0000000
FABP2 3.935419 1.761928 0.0000831 0.0002924
PMS2 6.484014 1.754823 0.0000000 0.0000000
BCL2 -14.203834 -1.743351 0.0000000 0.0000000
ICAM2 -6.219046 -1.733670 0.0000000 0.0000000
CXCR4 8.221892 1.704929 0.0000000 0.0000000
VWF -11.379797 -1.674150 0.0000000 0.0000000
E2F1 5.712391 1.672773 0.0000000 0.0000001
SERPINE1 18.441982 1.665830 0.0000000 0.0000000
THBD -9.178167 -1.646128 0.0000000 0.0000000
LRP1 33.818880 1.616986 0.0000000 0.0000000
PREX2 -8.964226 -1.616104 0.0000000 0.0000000
HLA-DPA1 2.704669 1.603870 0.0068373 0.0180880
TGFBI 16.283825 1.602270 0.0000000 0.0000000
CEBPB -27.630780 -1.599522 0.0000000 0.0000000
FZD7 -13.709425 -1.598140 0.0000000 0.0000000
CDKN1A -26.620935 -1.591218 0.0000000 0.0000000
MET -3.484660 -1.582995 0.0004928 0.0015496
MYC -15.907498 -1.581812 0.0000000 0.0000000
MMRN2 -11.302827 -1.564097 0.0000000 0.0000000
CSF3 -3.542786 -1.548903 0.0003959 0.0012609
MRC1 -2.769913 -1.514156 0.0056071 0.0149923
ANGPT1 12.068609 1.496008 0.0000000 0.0000000
IL1R2 -3.122143 -1.479563 0.0017954 0.0052806
NEDD4 -9.840310 -1.470373 0.0000000 0.0000000
ZAP70 8.459084 1.464578 0.0000000 0.0000000
S100A9 -3.248522 -1.442380 0.0011601 0.0034732
WNT3A -3.472153 -1.428151 0.0005163 0.0016134
CDK6 13.956409 1.407898 0.0000000 0.0000000
ROR1 5.070610 1.390886 0.0000004 0.0000017
TEK -3.674870 -1.336318 0.0002380 0.0007828
HIF1A 14.915801 1.327309 0.0000000 0.0000000
CLDN5 -7.738388 -1.325238 0.0000000 0.0000000
CX3CR1 -2.738425 -1.274203 0.0061734 0.0164187
FGF2 -2.891001 -1.269654 0.0038402 0.0109096
CDH5 -10.608042 -1.247664 0.0000000 0.0000000
BST2 -6.821553 -1.216097 0.0000000 0.0000000
IKZF2 5.432656 1.178209 0.0000001 0.0000003
TGFB3 19.313602 1.170899 0.0000000 0.0000000
SNAI1 -2.556620 -1.160005 0.0105695 0.0271012
CSF2 -3.951694 -1.125028 0.0000776 0.0002771
ATF3 -12.496110 -1.123431 0.0000000 0.0000000
LDHA -5.676017 -1.111902 0.0000000 0.0000001
FLT1 -4.239954 -1.111822 0.0000224 0.0000828
IFNAR2 2.904295 1.090806 0.0036808 0.0105166
PDGFRA -8.147789 -1.089376 0.0000000 0.0000000
IFITM1 -2.429198 -1.068436 0.0151323 0.0380208
IL23A -2.783304 -1.064441 0.0053808 0.0145386
NOS3 -3.302331 -1.064094 0.0009588 0.0029056
SLC13A3 3.282285 1.033184 0.0010297 0.0031015
INSR -22.110890 -1.001272 0.0000000 0.0000000
EPHA4 -3.719483 -1.001263 0.0001996 0.0006654

4.2 Cancer cell

names scores logfoldchanges pvals pvals_adj
FOS -9.674765 -18.332428 0.0000000 0.0000000
COL1A1 10.273704 15.094367 0.0000000 0.0000000
ATF3 -6.680579 -7.325389 0.0000000 0.0000000
JUNB -6.519753 -6.353756 0.0000000 0.0000000
EGR1 -6.436063 -4.904849 0.0000000 0.0000000
JUN -6.486479 -4.801098 0.0000000 0.0000000
DUSP1 -5.359185 -4.615851 0.0000001 0.0000052
FLT4 3.672781 4.157596 0.0002399 0.0074977
COL5A1 3.294915 3.599521 0.0009845 0.0259082
LMNA -3.604216 -3.569431 0.0003131 0.0092087
FN1 4.274744 3.321740 0.0000191 0.0007973
COL4A1 5.705288 3.206742 0.0000000 0.0000008
THBD -4.691177 -2.850006 0.0000027 0.0001235
PROX1 3.904441 2.778789 0.0000944 0.0036324
MYC -4.748903 -2.713153 0.0000020 0.0001023
EPHB4 5.087696 2.504998 0.0000004 0.0000201
ETS1 3.751177 2.027703 0.0001760 0.0058669
PKM 3.832851 2.000154 0.0001267 0.0045238
TGFB1 3.585058 1.682249 0.0003370 0.0093612
CDH5 3.114175 1.452822 0.0018446 0.0461150

4.3 Dendritic

names scores logfoldchanges pvals pvals_adj
NA NA NA NA NA
:—–: :——: :————–: :—–: :———:

4.4 Endothelial

names scores logfoldchanges pvals pvals_adj
VEGFA -35.816616 -10.077840 0.0000000 0.0000000
COL1A1 47.572320 9.932630 0.0000000 0.0000000
PLVAP 38.004112 9.664353 0.0000000 0.0000000
PDK4 -34.856445 -7.034097 0.0000000 0.0000000
COL4A1 35.776917 5.580956 0.0000000 0.0000000
PECAM1 27.437399 4.532059 0.0000000 0.0000000
SERPINE1 20.581670 4.145850 0.0000000 0.0000000
COL5A1 16.131900 4.142918 0.0000000 0.0000000
MMP11 3.607988 3.250464 0.0003086 0.0016072
KIT 3.419221 3.240729 0.0006280 0.0030785
RORC -14.886651 -3.145059 0.0000000 0.0000000
CXCL2 -4.145788 -3.131462 0.0000339 0.0002016
LMNA 28.933674 3.093195 0.0000000 0.0000000
ACTA2 10.422846 3.086447 0.0000000 0.0000000
PDGFRB 11.492411 2.996124 0.0000000 0.0000000
CD248 5.186810 2.958897 0.0000002 0.0000015
NEDD4 -14.398186 -2.812049 0.0000000 0.0000000
IL6R -14.629830 -2.766724 0.0000000 0.0000000
MMRN1 6.903936 2.753270 0.0000000 0.0000000
CD276 8.340302 2.740798 0.0000000 0.0000000
PPARGC1A -4.913524 -2.547583 0.0000009 0.0000060
TGFBR2 23.386492 2.544253 0.0000000 0.0000000
FN1 21.659600 2.516487 0.0000000 0.0000000
TGFB1 14.458306 2.510600 0.0000000 0.0000000
SH2D1B -3.437823 -2.446839 0.0005864 0.0029030
ENG 20.407070 2.388739 0.0000000 0.0000000
ETS1 20.198217 2.334731 0.0000000 0.0000000
CTSW 4.125513 2.294079 0.0000370 0.0002126
CLEC14A 20.905638 2.275434 0.0000000 0.0000000
TP63 -4.689392 -2.272294 0.0000027 0.0000176
E2F1 3.179068 2.174574 0.0014775 0.0067775
WWTR1 19.532927 2.166429 0.0000000 0.0000000
VWF 20.648241 2.120249 0.0000000 0.0000000
ITGA5 19.046722 2.072308 0.0000000 0.0000000
SELP 8.094025 2.045839 0.0000000 0.0000000
CD40 11.831773 2.011925 0.0000000 0.0000000
BAX 7.544480 1.991490 0.0000000 0.0000000
PGF 9.234379 1.901882 0.0000000 0.0000000
HIF1A 9.627744 1.900711 0.0000000 0.0000000
TNC 4.525780 1.900677 0.0000060 0.0000371
PDGFB 17.226614 1.887452 0.0000000 0.0000000
ADAMTS4 4.126706 1.855702 0.0000368 0.0002126
GPX3 -8.903686 -1.853876 0.0000000 0.0000000
BMP1 14.768687 1.831141 0.0000000 0.0000000
SFRP2 5.325660 1.798780 0.0000001 0.0000007
EPHB4 18.495956 1.784540 0.0000000 0.0000000
PREX2 10.391800 1.776872 0.0000000 0.0000000
CX3CL1 -4.940236 -1.758980 0.0000008 0.0000053
NRP1 13.158820 1.680857 0.0000000 0.0000000
STAT6 12.710796 1.661942 0.0000000 0.0000000
TGFBR3 6.681840 1.653359 0.0000000 0.0000000
LRP1 6.209331 1.609881 0.0000000 0.0000000
NOTCH1 13.198600 1.580802 0.0000000 0.0000000
EGFR -4.993105 -1.578319 0.0000006 0.0000041
TP53 5.333368 1.534384 0.0000001 0.0000007
CEBPB -12.922456 -1.513152 0.0000000 0.0000000
PIK3CG 3.390175 1.512210 0.0006985 0.0033907
NFKBIA -18.059793 -1.487747 0.0000000 0.0000000
BST2 -5.830517 -1.456533 0.0000000 0.0000000
MMRN2 15.647755 1.394302 0.0000000 0.0000000
MAFB -4.131586 -1.382667 0.0000360 0.0002119
HDAC1 9.211005 1.381150 0.0000000 0.0000000
FLT4 8.894653 1.355712 0.0000000 0.0000000
DUSP1 -7.505675 -1.349224 0.0000000 0.0000000
NOS3 8.390466 1.348691 0.0000000 0.0000000
SOD2 -6.459475 -1.338413 0.0000000 0.0000000
CDH5 14.235497 1.296522 0.0000000 0.0000000
LGALS9 3.786406 1.291265 0.0001528 0.0008307
STING1 4.681596 1.286953 0.0000028 0.0000178
TBX3 -3.312442 -1.264155 0.0009249 0.0044464
EPHA2 5.218903 1.226869 0.0000002 0.0000013
KDR 9.706591 1.213559 0.0000000 0.0000000
NCAM1 -3.591465 -1.157682 0.0003288 0.0016950
CDKN1A -9.336715 -1.154624 0.0000000 0.0000000
INSR 7.027732 1.133876 0.0000000 0.0000000
JUN -11.472332 -1.064434 0.0000000 0.0000000
IL3RA 4.837041 1.048972 0.0000013 0.0000086
TEAD4 4.684701 1.045321 0.0000028 0.0000177
IRF3 4.997752 1.042328 0.0000006 0.0000040
YAP1 -9.386043 -1.032338 0.0000000 0.0000000
CTNNB1 9.553021 1.020440 0.0000000 0.0000000

4.5 Fibroblast

names scores logfoldchanges pvals pvals_adj
COL1A1 99.661520 109.207320 0.0000000 0.0000000
FOS -47.059372 -10.880125 0.0000000 0.0000000
EGR1 -50.041943 -10.419629 0.0000000 0.0000000
FN1 58.055080 8.389499 0.0000000 0.0000000
JUN -63.418068 -7.511326 0.0000000 0.0000000
COL5A1 58.653736 6.514852 0.0000000 0.0000000
PDK4 -36.407936 -6.081756 0.0000000 0.0000000
GPX3 -34.492940 -5.962629 0.0000000 0.0000000
SERPINA1 9.758843 4.440912 0.0000000 0.0000000
CCR2 4.496484 3.799526 0.0000069 0.0000326
RET -3.050877 -3.763918 0.0022817 0.0082672
TNC 28.061033 3.746374 0.0000000 0.0000000
DUSP1 -42.866486 -3.717051 0.0000000 0.0000000
FLI1 4.938783 3.521752 0.0000008 0.0000040
SPRY2 -28.405836 -3.440419 0.0000000 0.0000000
BCL2 -21.041565 -3.361053 0.0000000 0.0000000
IL6R -11.209660 -3.353977 0.0000000 0.0000000
TNF 6.995335 3.302661 0.0000000 0.0000000
FAP 5.171738 3.295502 0.0000002 0.0000012
HLA-DPA1 2.532061 3.215192 0.0113394 0.0363443
KLF2 -22.494427 -3.147081 0.0000000 0.0000000
PREX2 -9.170182 -3.143904 0.0000000 0.0000000
TGFBI 14.967690 3.113704 0.0000000 0.0000000
PLA2G2A -10.403379 -2.908959 0.0000000 0.0000000
CR2 4.180466 2.905692 0.0000291 0.0001359
BMP1 42.859085 2.858506 0.0000000 0.0000000
EPHA2 -5.979615 -2.842888 0.0000000 0.0000000
EGFR -36.323550 -2.792461 0.0000000 0.0000000
TEAD4 4.601498 2.774775 0.0000042 0.0000202
LGR5 -5.319131 -2.760852 0.0000001 0.0000006
MMP11 10.715138 2.731303 0.0000000 0.0000000
PGF -6.036967 -2.727679 0.0000000 0.0000000
SOD2 -21.268118 -2.698692 0.0000000 0.0000000
NFKBIA -37.298576 -2.643214 0.0000000 0.0000000
CXCL1 5.260466 2.607160 0.0000001 0.0000008
S100A9 -3.774349 -2.586396 0.0001604 0.0006741
HGF 3.872809 2.472608 0.0001076 0.0004678
CLCA1 3.283746 2.400243 0.0010244 0.0040014
FZD7 -21.664896 -2.394277 0.0000000 0.0000000
JUNB -20.558294 -2.368409 0.0000000 0.0000000
CDK6 12.404665 2.341559 0.0000000 0.0000000
POU2AF1 10.431594 2.292325 0.0000000 0.0000000
CD1C 2.798475 2.265068 0.0051344 0.0171148
CXCL2 7.335484 2.252299 0.0000000 0.0000000
COL11A1 19.515144 2.240313 0.0000000 0.0000000
MET -2.514364 -2.211613 0.0119247 0.0379769
MMP9 8.479343 2.173744 0.0000000 0.0000000
ZAP70 7.108235 2.166870 0.0000000 0.0000000
COL4A1 -14.409939 -2.116672 0.0000000 0.0000000
MUC1 8.429799 2.110764 0.0000000 0.0000000
PDGFRA -24.080532 -2.103632 0.0000000 0.0000000
LOX 3.660348 2.065853 0.0002519 0.0010239
LGALS9 2.994693 2.004917 0.0027472 0.0097419
IL1R2 -3.184731 -2.000739 0.0014489 0.0054882
PROX1 -3.163278 -1.992363 0.0015600 0.0058210
SNAI1 -2.816050 -1.910241 0.0048618 0.0164250
EPHB3 8.673355 1.896608 0.0000000 0.0000000
PCNA 3.990071 1.889885 0.0000661 0.0002923
CD40 -14.321314 -1.875060 0.0000000 0.0000000
TGFBR3 -20.271786 -1.864158 0.0000000 0.0000000
PMS2 5.101554 1.863890 0.0000003 0.0000018
MYC -10.560474 -1.857794 0.0000000 0.0000000
FABP2 3.179310 1.830631 0.0014763 0.0055499
ANGPT1 10.989499 1.819680 0.0000000 0.0000000
CHEK2 5.127824 1.816907 0.0000003 0.0000015
PDGFB 3.672426 1.788692 0.0002403 0.0009847
STAT5A -9.828810 -1.781564 0.0000000 0.0000000
TGFB3 16.945640 1.773514 0.0000000 0.0000000
IRS1 21.651104 1.769264 0.0000000 0.0000000
CCL5 2.701328 1.763938 0.0069063 0.0227181
CEBPB -22.662645 -1.746426 0.0000000 0.0000000
ACTA2 8.518517 1.733649 0.0000000 0.0000000
FGF2 -3.000306 -1.725000 0.0026971 0.0096324
PDCD1LG2 -3.260586 -1.706443 0.0011118 0.0042762
NCAM1 -15.913406 -1.669092 0.0000000 0.0000000
ADAMTS4 2.454511 1.665744 0.0141076 0.0443636
DES -4.886082 -1.663549 0.0000010 0.0000051
INSR -20.385859 -1.617411 0.0000000 0.0000000
VEGFA -20.609896 -1.615722 0.0000000 0.0000000
CDH5 -2.543350 -1.572550 0.0109795 0.0354178
PTGS2 -5.282298 -1.533162 0.0000001 0.0000007
PTEN -3.068287 -1.522349 0.0021529 0.0078573
CD248 15.250261 1.477586 0.0000000 0.0000000
E2F1 3.785424 1.458056 0.0001534 0.0006614
IKZF2 4.658562 1.452231 0.0000032 0.0000155
RGMB -8.223030 -1.441226 0.0000000 0.0000000
CDKN1A -14.259747 -1.387398 0.0000000 0.0000000
ROR1 4.154857 1.339904 0.0000325 0.0001493
LDHA -5.042535 -1.325870 0.0000005 0.0000024
HLA-DPB1 -3.528480 -1.323532 0.0004180 0.0016718
AKT3 -8.580392 -1.308634 0.0000000 0.0000000
CLEC14A 5.388428 1.300371 0.0000001 0.0000004
IFNGR1 -5.820803 -1.280707 0.0000000 0.0000000
IGF1 -8.744483 -1.254595 0.0000000 0.0000000
HIF1A 9.534808 1.234161 0.0000000 0.0000000
CD276 11.619246 1.205276 0.0000000 0.0000000
MMP2 9.961576 1.204999 0.0000000 0.0000000
CAV1 -8.108888 -1.185997 0.0000000 0.0000000
TGFBR2 -16.892298 -1.173018 0.0000000 0.0000000
NFE2L2 -8.193779 -1.172432 0.0000000 0.0000000
CSF2 -2.866087 -1.156208 0.0041558 0.0142322
CCND1 3.267800 1.152726 0.0010839 0.0042010
TGFB1 6.314698 1.150336 0.0000000 0.0000000
DKK1 -3.892902 -1.115128 0.0000991 0.0004344
SOX9 -2.426580 -1.105025 0.0152419 0.0470428
LRP5 -6.391503 -1.060284 0.0000000 0.0000000
AMOTL2 -10.678584 -1.059197 0.0000000 0.0000000
SERPINE1 11.867847 1.043810 0.0000000 0.0000000
PKM 15.817124 1.039588 0.0000000 0.0000000
CXCL16 -3.090467 -1.039031 0.0019984 0.0073471
STING1 -4.668215 -1.027912 0.0000030 0.0000149
FGFR1 -19.189692 -1.024236 0.0000000 0.0000000
CTNNB1 12.186530 1.021446 0.0000000 0.0000000
MFAP5 -6.680034 -1.017788 0.0000000 0.0000000
AXIN2 5.655657 1.006511 0.0000000 0.0000001

4.6 Macrophage

names scores logfoldchanges pvals pvals_adj
COL1A1 29.665201 21.313148 0.0000000 0.0000000
FOS -22.637910 -12.442084 0.0000000 0.0000000
MMP9 5.213645 6.499431 0.0000002 0.0000044
SPP1 4.578217 6.127543 0.0000047 0.0000977
FN1 17.229155 5.819446 0.0000000 0.0000000
EGR1 -17.853518 -4.971041 0.0000000 0.0000000
TREM2 5.923193 4.002033 0.0000000 0.0000001
PDK4 -14.654759 -3.942336 0.0000000 0.0000000
MRC1 -16.989233 -3.646870 0.0000000 0.0000000
ITGAX 13.298241 3.640879 0.0000000 0.0000000
COL5A1 10.114567 3.443203 0.0000000 0.0000000
DUSP1 -13.914675 -2.867081 0.0000000 0.0000000
THBD -8.767480 -2.502315 0.0000000 0.0000000
CD248 3.794988 2.477330 0.0001477 0.0018006
PKM 11.442293 2.380384 0.0000000 0.0000000
HIF1A 5.919156 2.233082 0.0000000 0.0000001
LRP1 12.007602 2.061832 0.0000000 0.0000000
CD276 3.925850 1.964722 0.0000864 0.0012003
FCGR3A 3.039158 1.703409 0.0023724 0.0237241
JUN -3.627001 -1.703343 0.0002867 0.0034135
FCER2 -3.336796 -1.691925 0.0008475 0.0096307
LYZ 4.354130 1.606014 0.0000134 0.0002672
IDH1 4.306766 1.557988 0.0000166 0.0003037
CCL4 -2.795289 -1.526315 0.0051853 0.0480124
SOD2 3.880743 1.394751 0.0001041 0.0013351
HLA-DRA 6.996792 1.373868 0.0000000 0.0000000
JUNB -7.531564 -1.357233 0.0000000 0.0000000
MYC -4.065466 -1.342558 0.0000479 0.0007490
ITGB1 3.865934 1.315215 0.0001107 0.0013833
CD163 -7.874438 -1.234347 0.0000000 0.0000000
CSF3R 6.345931 1.167912 0.0000000 0.0000000
CXCR4 6.013884 1.144618 0.0000000 0.0000001
ENG 2.912792 1.120543 0.0035821 0.0344436
CDK6 3.298332 1.119680 0.0009726 0.0105719
STAT5A 4.015679 1.092700 0.0000593 0.0008592
CEBPB -6.055065 -1.052671 0.0000000 0.0000000
VEGFB 3.265556 1.012063 0.0010925 0.0116223

4.7 Mast cell

names scores logfoldchanges pvals pvals_adj
COL1A1 11.554090 30.175860 0.0000000 0.0000000
FN1 3.923991 4.566871 0.0000871 0.0075897
VEGFA -6.816688 -4.331221 0.0000000 0.0000000
COL5A1 3.746050 4.181580 0.0001796 0.0128315
SFRP2 3.621788 4.016486 0.0002926 0.0182859
NFKB2 -6.765123 -3.871854 0.0000000 0.0000000
ICAM1 -4.836095 -2.638979 0.0000013 0.0001655
CSF1 3.913213 2.463667 0.0000911 0.0075897

4.8 Smooth Muscle cell

names scores logfoldchanges pvals pvals_adj
COL1A1 36.033295 35.535330 0.0000000 0.0000000
COL4A1 27.172250 7.101044 0.0000000 0.0000000
FOS -14.032536 -6.647189 0.0000000 0.0000000
JUN -15.592484 -5.803882 0.0000000 0.0000000
FN1 18.829844 5.127449 0.0000000 0.0000000
TNF 4.487255 4.998678 0.0000072 0.0000863
COL5A1 21.033014 4.751438 0.0000000 0.0000000
ACTA2 -14.657331 -4.576652 0.0000000 0.0000000
JUNB -17.292665 -4.422530 0.0000000 0.0000000
LGR6 -5.308680 -4.066671 0.0000001 0.0000017
MYH11 -15.415986 -4.019932 0.0000000 0.0000000
PDGFRB 11.228720 3.559115 0.0000000 0.0000000
CHEK2 2.926007 3.364132 0.0034334 0.0264110
PDK4 -9.583596 -3.270993 0.0000000 0.0000000
PTGDR2 -2.747317 -3.097388 0.0060085 0.0406734
DUSP1 -14.434421 -3.063678 0.0000000 0.0000000
SERPINE1 9.548772 3.017724 0.0000000 0.0000000
E2F1 3.277156 2.942244 0.0010486 0.0095326
ATF3 -11.208811 -2.790443 0.0000000 0.0000000
PLVAP 6.595327 2.787905 0.0000000 0.0000000
MMP11 7.006973 2.598386 0.0000000 0.0000000
BMP1 14.924097 2.452774 0.0000000 0.0000000
CX3CL1 -3.627839 -2.451389 0.0002858 0.0029164
CD248 13.306128 2.423763 0.0000000 0.0000000
ICAM3 4.481207 2.389812 0.0000074 0.0000863
DES -6.431553 -2.373101 0.0000000 0.0000000
SFRP2 5.309166 2.353069 0.0000001 0.0000017
MYBL2 2.944799 2.263086 0.0032316 0.0256479
CD276 6.821728 2.071905 0.0000000 0.0000000
TEAD4 2.747155 1.998582 0.0060115 0.0406734
IL6R -4.582089 -1.868957 0.0000046 0.0000606
MCM6 2.795881 1.806143 0.0051758 0.0369703
CDKN1A -11.316127 -1.774034 0.0000000 0.0000000
KLF2 -5.610818 -1.752987 0.0000000 0.0000003
CLEC14A 3.085336 1.746859 0.0020332 0.0169435
NRP1 9.378545 1.654721 0.0000000 0.0000000
TAP2 4.574986 1.648253 0.0000048 0.0000611
LMNA 8.512371 1.593157 0.0000000 0.0000000
SOCS3 6.051931 1.562556 0.0000000 0.0000000
ACKR3 -4.485043 -1.531240 0.0000073 0.0000863
HLA-B 8.327289 1.479265 0.0000000 0.0000000
CDCA7 3.018203 1.449249 0.0025428 0.0208425
ENG 3.458363 1.406951 0.0005435 0.0053281
TGFB1 6.001135 1.390858 0.0000000 0.0000000
TGFBI 4.974090 1.370771 0.0000007 0.0000094
ETS1 7.227550 1.338475 0.0000000 0.0000000
GPX3 -5.156676 -1.281363 0.0000003 0.0000037
SMOC2 4.394368 1.269092 0.0000111 0.0001262
THBD 2.854734 1.213459 0.0043073 0.0319210
ITGA5 4.251924 1.196920 0.0000212 0.0002304
ITGA1 3.349972 1.165580 0.0008082 0.0076245
TEAD1 3.748163 1.138734 0.0001781 0.0018950
EPHB4 3.485354 1.100657 0.0004915 0.0049149
AKT1 6.131342 1.046931 0.0000000 0.0000000

4.9 T cell

names scores logfoldchanges pvals pvals_adj
COL1A1 18.528063 34.526530 0.0000000 0.0000000
FN1 8.459756 5.744955 0.0000000 0.0000000
CD40LG -5.212253 -2.767354 0.0000002 0.0000311
FOS -3.901277 -2.126768 0.0000957 0.0053159
COL5A1 4.896749 2.073000 0.0000010 0.0000974
CTSW 3.538528 2.022379 0.0004024 0.0167652
CCL5 3.458697 1.933948 0.0005428 0.0208767
LMNA -3.985240 -1.488541 0.0000674 0.0042133
IL2RB 3.246724 1.352781 0.0011674 0.0389138
CCR4 -4.940328 -1.278427 0.0000008 0.0000974
ITK -4.046594 -1.261162 0.0000520 0.0037120
NFKBIA -4.168602 -1.091386 0.0000306 0.0025540

5. Gene differentiation (Cancer cell v.s. Other cells)

Here, we use Wilcoxon rank-sum test to compute gene differential expression (DE). P value are adjusted using Benjamini–Hochberg procedure. The statistical significance was cut-off by log2(Fold Change) > 2 or log2(Fold Change) < -2 and p_value < 0.05.

The result are visualized via Volcano plot: a type of scatterplot that shows statistical significance (P value) versus magnitude of change (fold change).

The comparison is between Cancer cells and Otehr cell types. A positive fold change means higher expression in the cancer cells.

5.1 all

names scores logfoldchanges pvals pvals_adj
COL1A1 -30.234367 -66.372210 0.0000000 0.0000000
FLT4 49.202785 15.788570 0.0000000 0.0000000
MMRN1 39.836563 10.758931 0.0000000 0.0000000
PROX1 39.153530 9.631906 0.0000000 0.0000000
CLDN5 32.387257 6.232538 0.0000000 0.0000000
COL5A1 -27.786400 -5.870316 0.0000000 0.0000000
PECAM1 33.999645 5.581362 0.0000000 0.0000000
CDH5 32.039720 5.392687 0.0000000 0.0000000
EPHB4 35.269524 5.347107 0.0000000 0.0000000
EPHA2 24.365593 5.331178 0.0000000 0.0000000
TGFBR2 32.012127 5.102354 0.0000000 0.0000000
LRP1 -27.004213 -5.021764 0.0000000 0.0000000
CEACAM1 4.158547 4.977080 0.0000320 0.0001586
NOTCH1 30.316938 4.929549 0.0000000 0.0000000
ANGPT2 12.962784 4.763260 0.0000000 0.0000000
LRP5 27.294119 4.496007 0.0000000 0.0000000
C1QC -2.606720 -4.462786 0.0091414 0.0346266
VWF 26.617043 4.261424 0.0000000 0.0000000
CCL2 7.665418 4.228971 0.0000000 0.0000000
IRS1 -12.957179 -4.099947 0.0000000 0.0000000
SFRP2 -15.366248 -3.979915 0.0000000 0.0000000
POU2AF1 -5.700474 -3.800232 0.0000000 0.0000001
DES -2.480227 -3.765591 0.0131299 0.0468752
SMOC2 -4.808911 -3.636970 0.0000015 0.0000082
EGR1 -8.862293 -3.463138 0.0000000 0.0000000
COL11A1 -8.488113 -3.386990 0.0000000 0.0000000
WWTR1 24.163424 3.360926 0.0000000 0.0000000
THBD 17.416860 3.311530 0.0000000 0.0000000
LAMC2 8.324216 3.255252 0.0000000 0.0000000
FZD7 -4.040922 -3.246518 0.0000532 0.0002560
ETS1 22.821505 3.218561 0.0000000 0.0000000
MAFB -6.304635 -3.160458 0.0000000 0.0000000
KDR 15.949995 3.149618 0.0000000 0.0000000
FOS -8.181387 -3.000704 0.0000000 0.0000000
CD248 -12.422921 -2.965086 0.0000000 0.0000000
MRC1 17.068316 2.927383 0.0000000 0.0000000
LGALS9 12.149327 2.901178 0.0000000 0.0000000
FBLN1 -6.271950 -2.899141 0.0000000 0.0000000
KLF2 17.547354 2.879732 0.0000000 0.0000000
STAT6 -11.564986 -2.873346 0.0000000 0.0000000
XBP1 -2.573265 -2.855613 0.0100744 0.0375911
FN1 -4.631436 -2.850724 0.0000036 0.0000191
CXCL12 -4.834656 -2.832815 0.0000013 0.0000072
IL3RA 4.264347 2.813612 0.0000200 0.0001002
SERPINA1 -3.110643 -2.774476 0.0018668 0.0078437
ADAMTS4 9.780691 2.758544 0.0000000 0.0000000
CCND1 9.422385 2.728789 0.0000000 0.0000000
PDGFRA -6.505960 -2.673367 0.0000000 0.0000000
PDGFB 13.543466 2.656035 0.0000000 0.0000000
TGFB1 18.663588 2.643694 0.0000000 0.0000000
PDGFA 4.470575 2.634153 0.0000078 0.0000406
CXCR4 -2.907358 -2.627028 0.0036450 0.0146974
MFAP5 -2.876015 -2.624575 0.0040273 0.0161092
VEGFA -8.933245 -2.616318 0.0000000 0.0000000
EGFR -6.038542 -2.547140 0.0000000 0.0000000
NRP1 -8.648032 -2.542835 0.0000000 0.0000000
SOCS3 14.483997 2.452043 0.0000000 0.0000000
LAMP3 3.676615 2.374362 0.0002363 0.0010842
NFKB2 14.192906 2.351859 0.0000000 0.0000000
ENG 13.960588 2.322109 0.0000000 0.0000000
ACKR3 10.755397 2.317773 0.0000000 0.0000000
WNT5A 7.827144 2.296896 0.0000000 0.0000000
CAV1 12.607881 2.295816 0.0000000 0.0000000
ITGA5 17.585703 2.232826 0.0000000 0.0000000
NFKBIA 16.100695 2.228696 0.0000000 0.0000000
JUNB 14.978644 2.220200 0.0000000 0.0000000
PDGFRB -12.107302 -2.177165 0.0000000 0.0000000
COL4A1 21.848337 2.176294 0.0000000 0.0000000
ERBB2 -3.849126 -2.173088 0.0001185 0.0005539
HDAC1 12.438637 2.164805 0.0000000 0.0000000
TP53 7.972046 2.156289 0.0000000 0.0000000
MMP9 -2.724283 -2.102251 0.0064441 0.0247851
PDPN 9.206426 1.990355 0.0000000 0.0000000
COL6A3 -2.951266 -1.975311 0.0031647 0.0129703
TNC -5.974151 -1.928164 0.0000000 0.0000000
HLA-B 14.376368 1.922179 0.0000000 0.0000000
NOS3 3.230716 1.904751 0.0012348 0.0053224
PGF 7.104472 1.858123 0.0000000 0.0000000
BAX 8.752142 1.847590 0.0000000 0.0000000
MMP2 -4.664866 -1.843612 0.0000031 0.0000164
JAK1 12.517763 1.804875 0.0000000 0.0000000
ZAP70 -2.805611 -1.794658 0.0050221 0.0197651
SMO -3.288672 -1.793463 0.0010066 0.0043766
CD40 -3.303482 -1.787516 0.0009549 0.0041882
VSIR 4.959197 1.785986 0.0000007 0.0000039
SOD2 6.086195 1.783705 0.0000000 0.0000000
TEK 2.516400 1.753822 0.0118561 0.0435885
AXIN2 -3.143348 -1.736542 0.0016703 0.0071379
MYBL2 2.803198 1.722033 0.0050599 0.0197651
STAT5A 8.228669 1.700959 0.0000000 0.0000000
BCL2L1 11.443256 1.617904 0.0000000 0.0000000
CEBPB -5.715006 -1.611982 0.0000000 0.0000001
KRAS 2.697715 1.603659 0.0069817 0.0266478
IKBKB 9.370044 1.595195 0.0000000 0.0000000
HLA-C 9.546324 1.587844 0.0000000 0.0000000
BMP1 -9.764231 -1.586375 0.0000000 0.0000000
ICAM2 3.878212 1.564105 0.0001052 0.0004964
NFKB1 5.290005 1.556090 0.0000001 0.0000007
SERPINE1 5.126382 1.549977 0.0000003 0.0000017
MYC 7.662256 1.499068 0.0000000 0.0000000
RELA 9.570774 1.401174 0.0000000 0.0000000
CDK2 5.330290 1.380223 0.0000001 0.0000006
TEAD4 4.466981 1.378127 0.0000079 0.0000409
PPARD 5.854594 1.352328 0.0000000 0.0000000
TAPBP 6.916269 1.319036 0.0000000 0.0000000
PKM 11.654527 1.313473 0.0000000 0.0000000
TGFBR3 6.730128 1.276004 0.0000000 0.0000000
TGFBI -3.645394 -1.246905 0.0002670 0.0012136
EPHB3 -2.477819 -1.239326 0.0132188 0.0468752
DUSP1 10.725418 1.235634 0.0000000 0.0000000
DNMT3A 4.041825 1.188595 0.0000530 0.0002560
PLVAP 4.334969 -1.157218 0.0000146 0.0000736
HRAS 4.012735 1.152498 0.0000600 0.0002858
HIF1A 6.254380 1.105747 0.0000000 0.0000000
STING1 2.921010 1.074498 0.0034890 0.0141829
TAP2 5.652274 1.006036 0.0000000 0.0000001

5.2 Dendritic

names scores logfoldchanges pvals pvals_adj
ADAMTS4 5.575643 28.643430 0.0000000 0.0000002
FLT4 22.930662 15.196451 0.0000000 0.0000000
CCR7 -13.284574 -10.923151 0.0000000 0.0000000
PROX1 18.395388 10.410879 0.0000000 0.0000000
CIITA -17.329952 -9.570079 0.0000000 0.0000000
MMRN1 18.056110 8.623397 0.0000000 0.0000000
CSF2RA -8.679269 -7.977796 0.0000000 0.0000000
HLA-DRA -16.502650 -7.942287 0.0000000 0.0000000
CXCR4 -16.693066 -7.523554 0.0000000 0.0000000
VWF 13.605382 6.950786 0.0000000 0.0000000
TNFRSF13C -10.914473 -6.930525 0.0000000 0.0000000
IRF4 -7.556554 -6.864675 0.0000000 0.0000000
CD79A -9.998557 -6.843328 0.0000000 0.0000000
EPHB4 17.560500 6.689251 0.0000000 0.0000000
CLDN5 15.297259 6.589192 0.0000000 0.0000000
TGFBR3 5.780132 6.537902 0.0000000 0.0000001
LAMP3 -8.201576 -6.439131 0.0000000 0.0000000
CDH5 15.522088 6.420683 0.0000000 0.0000000
CD83 -10.204256 -6.304693 0.0000000 0.0000000
HLA-DRB1 -5.456577 -6.121566 0.0000000 0.0000004
IDO1 -4.211938 -6.069129 0.0000253 0.0001666
ANGPT2 6.259144 5.728770 0.0000000 0.0000000
EPHA2 11.486605 5.686294 0.0000000 0.0000000
PECAM1 15.072761 5.671282 0.0000000 0.0000000
HLA-DPB1 -13.790742 -5.628202 0.0000000 0.0000000
MS4A1 -8.077124 -5.588415 0.0000000 0.0000000
IDO2 -4.387294 -5.544015 0.0000115 0.0000808
COL4A1 12.923530 5.535046 0.0000000 0.0000000
BLK -8.614294 -5.472012 0.0000000 0.0000000
LRP5 13.498300 5.385929 0.0000000 0.0000000
POU2AF1 -7.675400 -5.383527 0.0000000 0.0000000
PDCD1LG2 -3.225880 -5.377147 0.0012559 0.0064074
KDR 8.599012 5.282702 0.0000000 0.0000000
COL1A1 -3.627274 -5.266028 0.0002864 0.0016274
TGFBR2 14.809233 5.192122 0.0000000 0.0000000
CD27 -3.687631 -5.159600 0.0002264 0.0013315
LAMC2 4.310445 5.094597 0.0000163 0.0001086
HLA-DMA -9.222815 -5.058350 0.0000000 0.0000000
SERPINE1 5.723733 4.946672 0.0000000 0.0000001
CYBB -4.493606 -4.852168 0.0000070 0.0000500
CAV1 7.927054 4.720061 0.0000000 0.0000000
THBD 8.934001 4.700087 0.0000000 0.0000000
CD79B -5.542990 -4.584476 0.0000000 0.0000002
ITGA5 11.229123 4.533934 0.0000000 0.0000000
PDGFB 7.566119 4.508731 0.0000000 0.0000000
WWTR1 12.832059 4.428220 0.0000000 0.0000000
NOTCH1 13.431126 4.346709 0.0000000 0.0000000
MRC1 8.466534 4.336106 0.0000000 0.0000000
CD40 -8.365058 -4.305286 0.0000000 0.0000000
FN1 10.865660 4.299931 0.0000000 0.0000000
ITGB2 -6.631293 -4.290758 0.0000000 0.0000000
ENG 8.182227 4.284961 0.0000000 0.0000000
CD19 -3.656628 -4.261206 0.0002556 0.0014858
NEDD4 2.608453 4.136596 0.0090952 0.0392037
PGF 4.205232 4.126223 0.0000261 0.0001694
MZB1 -3.530306 -3.957303 0.0004151 0.0023060
TNFRSF13B -4.023500 -3.915751 0.0000573 0.0003584
STAT6 -9.996908 -3.857708 0.0000000 0.0000000
CCL2 3.259852 3.719294 0.0011147 0.0058058
ITGA4 -3.161675 -3.705057 0.0015686 0.0078432
TCF7L2 6.047178 3.648106 0.0000000 0.0000000
FOS 5.408423 3.627001 0.0000001 0.0000005
STING1 2.565906 3.574186 0.0102907 0.0436045
LMNA 10.652044 3.474922 0.0000000 0.0000000
XBP1 -4.326386 -3.468849 0.0000152 0.0001024
PDPN 5.780682 3.438046 0.0000000 0.0000001
BCL2 -5.564429 -3.313020 0.0000000 0.0000002
YAP1 10.258237 3.304194 0.0000000 0.0000000
IL4I1 -2.659356 -3.210551 0.0078290 0.0340393
CSF1 5.577512 3.205203 0.0000000 0.0000002
EGR1 5.875011 3.122147 0.0000000 0.0000000
TEAD4 3.075261 3.088758 0.0021032 0.0102096
ACKR3 5.734067 3.045517 0.0000000 0.0000001
FGFR1 7.266860 3.041884 0.0000000 0.0000000
CD22 -4.100348 -3.000063 0.0000413 0.0002611
SOCS3 6.930332 2.900397 0.0000000 0.0000000
BCL2L1 7.764342 2.839695 0.0000000 0.0000000
CCND1 4.550885 2.813689 0.0000053 0.0000387
JUN 7.548089 2.691194 0.0000000 0.0000000
ICAM3 -4.349254 -2.671456 0.0000137 0.0000949
JUNB 6.921977 2.612937 0.0000000 0.0000000
KLF2 6.993328 2.415148 0.0000000 0.0000000
MYC 4.339250 2.383519 0.0000143 0.0000979
TEAD1 3.882886 2.376347 0.0001032 0.0006144
PLVAP 3.485890 2.366507 0.0004905 0.0026371
CD276 3.298881 2.278342 0.0009707 0.0051090
LRP6 2.874400 2.271783 0.0040480 0.0189157
PTK2 3.510846 2.160695 0.0004467 0.0024543
ITGAM -2.556671 -2.131371 0.0105679 0.0444030
DNMT3A 2.826356 2.108640 0.0047081 0.0215968
CDKN1A -3.607484 -2.086196 0.0003092 0.0017370
ETS1 6.929122 2.062357 0.0000000 0.0000000
DUSP1 7.990050 2.050011 0.0000000 0.0000000
IL6R -3.634310 -2.016604 0.0002787 0.0016019
PIK3CG -3.906193 -1.848166 0.0000938 0.0005648
WNT5A 3.361107 1.808354 0.0007763 0.0041293
BMP1 5.542660 1.744531 0.0000000 0.0000002
CDK6 2.818770 1.659098 0.0048208 0.0217154
CDK2 2.782049 1.601205 0.0054017 0.0239012
HDAC3 3.143095 1.581246 0.0016717 0.0082758
CDK4 3.216095 1.485701 0.0012995 0.0065630
TGFB3 3.488748 1.485001 0.0004853 0.0026371
TGFB1 5.598950 1.476710 0.0000000 0.0000002
TP53 2.901555 1.388258 0.0037132 0.0175149
HLA-B -5.636220 -1.331809 0.0000000 0.0000001
CTNNB1 5.617310 1.322099 0.0000000 0.0000002
PPARD 2.690139 1.285442 0.0071422 0.0313256
RELA 4.161696 1.243916 0.0000316 0.0002025
BAX 3.026668 1.226085 0.0024727 0.0118878
NFKBIA 3.993816 1.198308 0.0000650 0.0004013
HIF1A 2.843506 1.120562 0.0044620 0.0206575
TAP2 -3.968529 -1.112809 0.0000723 0.0004410
PKM 4.568146 1.090755 0.0000049 0.0000362
NFKB1 -2.566346 -1.065200 0.0102776 0.0436045
HDAC1 3.118248 1.026530 0.0018193 0.0089181
LGALS9 3.228519 1.003901 0.0012443 0.0064074

5.3 Endothelial

names scores logfoldchanges pvals pvals_adj
FLT4 44.703564 12.865293 0.0000000 0.0000000
PROX1 36.386800 8.606276 0.0000000 0.0000000
MMRN1 35.857483 8.379796 0.0000000 0.0000000
PLVAP -19.834154 -8.279273 0.0000000 0.0000000
DES -17.248142 -8.051526 0.0000000 0.0000000
COL1A1 19.803497 7.758353 0.0000000 0.0000000
VEGFA -13.930445 -7.388773 0.0000000 0.0000000
MRC1 18.102749 6.962892 0.0000000 0.0000000
PDK4 -14.636215 -5.778185 0.0000000 0.0000000
FN1 23.469608 4.548699 0.0000000 0.0000000
RORC -6.578991 -3.775445 0.0000000 0.0000000
CCL2 6.961859 3.752752 0.0000000 0.0000000
PDPN 11.461261 3.688082 0.0000000 0.0000000
CEACAM1 3.696628 3.680882 0.0002185 0.0011746
WNT5A 8.609529 3.650680 0.0000000 0.0000000
ANGPT2 11.227932 3.618977 0.0000000 0.0000000
CIITA -3.658576 -3.602416 0.0002536 0.0013490
EPHA2 19.977839 3.575732 0.0000000 0.0000000
CX3CL1 -3.805867 -3.405912 0.0001413 0.0007850
LAMC2 7.867083 3.308665 0.0000000 0.0000000
CLDN5 21.868885 3.189516 0.0000000 0.0000000
MMRN2 -13.826021 -3.060329 0.0000000 0.0000000
EPHB4 23.449179 2.996217 0.0000000 0.0000000
TGFBR2 20.164034 2.957504 0.0000000 0.0000000
ACKR3 11.423423 2.937170 0.0000000 0.0000000
NCAM1 -3.368260 -2.924837 0.0007564 0.0038204
NRP1 -9.434331 -2.908634 0.0000000 0.0000000
LRP5 20.664236 2.846996 0.0000000 0.0000000
EPHA4 -4.139149 -2.845776 0.0000349 0.0002075
CD40 -6.823543 -2.842304 0.0000000 0.0000000
NOTCH1 21.069942 2.754266 0.0000000 0.0000000
CLEC14A -11.248166 -2.730251 0.0000000 0.0000000
ADAMTS4 8.786348 2.588556 0.0000000 0.0000000
TGFB1 17.312790 2.585994 0.0000000 0.0000000
CCND1 8.731067 2.559674 0.0000000 0.0000000
LGALS9 10.633161 2.539114 0.0000000 0.0000000
BST2 -5.374084 -2.513016 0.0000001 0.0000005
STAT6 -7.931891 -2.445001 0.0000000 0.0000000
SELP -3.865033 -2.391168 0.0001111 0.0006384
CEBPB -7.249545 -2.362703 0.0000000 0.0000000
FOS -10.023185 -2.319338 0.0000000 0.0000000
INSR -12.770866 -2.279513 0.0000000 0.0000000
LAMP3 3.054945 2.267794 0.0022510 0.0108222
HLA-DMA -2.897577 -2.177008 0.0037606 0.0169395
GPX3 -4.696518 -2.120563 0.0000026 0.0000172
HLA-DRA -4.095082 -2.034782 0.0000422 0.0002482
EGR1 -4.402620 -2.026428 0.0000107 0.0000668
IL6R -5.244992 -2.021764 0.0000002 0.0000011
PRKCA 2.902847 1.958296 0.0036979 0.0168085
SFRP2 6.683397 1.942264 0.0000000 0.0000000
ETS1 14.680700 1.938305 0.0000000 0.0000000
SRC 2.633546 1.902775 0.0084498 0.0370607
CDH5 15.824621 1.884149 0.0000000 0.0000000
PDGFA 3.573934 1.865215 0.0003517 0.0018508
NFKB2 11.423796 1.861532 0.0000000 0.0000000
WWTR1 15.130322 1.840414 0.0000000 0.0000000
FGFR1 10.571516 1.827248 0.0000000 0.0000000
SNAI2 3.127626 1.701708 0.0017622 0.0086384
PREX2 -4.751294 -1.698687 0.0000020 0.0000133
CSF1 8.015272 1.652306 0.0000000 0.0000000
COL5A1 5.716839 1.625909 0.0000000 0.0000001
TGFBI 2.588297 1.589357 0.0096452 0.0415741
BAX 7.584454 1.588793 0.0000000 0.0000000
FLT1 -2.559416 -1.480917 0.0104848 0.0448069
TP53 5.963479 1.460928 0.0000000 0.0000000
HIF1A 7.490570 1.445360 0.0000000 0.0000000
YAP1 11.637912 1.438263 0.0000000 0.0000000
TNC 3.743432 1.394424 0.0001815 0.0009865
JUN -9.453348 -1.389132 0.0000000 0.0000000
STAT5A 6.719129 1.381092 0.0000000 0.0000000
IFNGR2 5.177047 1.366359 0.0000002 0.0000015
NFKB1 4.490648 1.345947 0.0000071 0.0000449
TGFBR3 6.802820 1.309575 0.0000000 0.0000000
NEDD4 -3.434463 -1.289280 0.0005937 0.0030605
ELN 3.504167 1.278749 0.0004580 0.0023856
HDAC1 8.014704 1.248903 0.0000000 0.0000000
CDK4 5.766309 1.246479 0.0000000 0.0000001
SERPINE1 3.396882 1.228594 0.0006816 0.0034775
IRF3 6.152243 1.226308 0.0000000 0.0000000
TGFB3 7.423753 1.169281 0.0000000 0.0000000
ICAM1 -3.005546 -1.148246 0.0026510 0.0122734
NOS3 -3.816797 -1.138719 0.0001352 0.0007595
KDR 8.540455 1.135648 0.0000000 0.0000000
CD276 4.617243 1.094183 0.0000039 0.0000249
TAPBP 5.651355 1.093660 0.0000000 0.0000001
ICAM2 -3.023488 -1.064234 0.0024988 0.0117868
THBD 7.481168 1.046702 0.0000000 0.0000000
VSIR 3.117389 1.032336 0.0018246 0.0088573
DNMT3A 3.354050 1.015540 0.0007964 0.0039819
JAK1 7.317473 1.007920 0.0000000 0.0000000

5.4 Fibroblast

names scores logfoldchanges pvals pvals_adj
COL1A1 -42.731052 -93.822110 0.0000000 0.0000000
FLT4 49.256050 17.725115 0.0000000 0.0000000
MMRN1 40.000065 12.231711 0.0000000 0.0000000
PECAM1 39.804745 10.788208 0.0000000 0.0000000
PROX1 39.040077 9.672133 0.0000000 0.0000000
CDH5 33.798180 8.064749 0.0000000 0.0000000
VWF 29.629345 8.055489 0.0000000 0.0000000
CLDN5 33.521340 7.927781 0.0000000 0.0000000
COL5A1 -38.002243 -7.829512 0.0000000 0.0000000
MRC1 19.141650 6.776446 0.0000000 0.0000000
EPHA2 25.067492 6.523871 0.0000000 0.0000000
NOTCH1 32.074394 6.476636 0.0000000 0.0000000
ANGPT2 13.454915 6.019546 0.0000000 0.0000000
LRP1 -34.248690 -6.014241 0.0000000 0.0000000
EPHB4 36.054947 5.817259 0.0000000 0.0000000
CEACAM1 4.211778 5.753977 0.0000253 0.0001131
TGFBR2 33.457530 5.577415 0.0000000 0.0000000
SFRP2 -22.719910 -5.154109 0.0000000 0.0000000
FN1 -14.127425 -5.089942 0.0000000 0.0000000
THBD 19.372856 4.985294 0.0000000 0.0000000
CCL2 7.914473 4.785276 0.0000000 0.0000000
LRP5 27.618275 4.744786 0.0000000 0.0000000
COL4A1 26.326843 4.694160 0.0000000 0.0000000
IRS1 -16.804136 -4.583208 0.0000000 0.0000000
IL3RA 4.868235 4.537504 0.0000011 0.0000057
EGR1 -12.029412 -4.271424 0.0000000 0.0000000
NOS3 4.123110 4.201922 0.0000374 0.0001654
LAMP3 3.973283 4.197155 0.0000709 0.0003029
ETS1 25.448177 4.148090 0.0000000 0.0000000
ICAM2 5.289952 4.080911 0.0000001 0.0000007
PLVAP 8.101640 4.069229 0.0000000 0.0000000
PDGFB 15.616067 4.047020 0.0000000 0.0000000
COL11A1 -12.331130 -3.973780 0.0000000 0.0000000
SMOC2 -5.851472 -3.948786 0.0000000 0.0000000
KLF2 19.405684 3.753717 0.0000000 0.0000000
PGF 8.895370 3.734481 0.0000000 0.0000000
MMRN2 6.106821 3.718868 0.0000000 0.0000000
KDR 16.585400 3.616639 0.0000000 0.0000000
VSIR 6.676537 3.608885 0.0000000 0.0000000
LGALS9 13.032649 3.604638 0.0000000 0.0000000
FZD7 -5.056423 -3.588272 0.0000004 0.0000022
HLA-B 19.528645 3.566927 0.0000000 0.0000000
ADAMTS4 10.354584 3.561167 0.0000000 0.0000000
TGFB1 21.615849 3.539755 0.0000000 0.0000000
WWTR1 24.588570 3.538723 0.0000000 0.0000000
CD248 -16.020100 -3.431371 0.0000000 0.0000000
FBLN1 -8.803069 -3.386446 0.0000000 0.0000000
ENG 15.739862 3.332966 0.0000000 0.0000000
FOS -7.632285 -3.263725 0.0000000 0.0000000
POU2AF1 -5.736293 -3.221704 0.0000000 0.0000001
PDGFRA -9.429633 -3.189484 0.0000000 0.0000000
SERPINA1 -4.109347 -3.143462 0.0000397 0.0001740
CXCL12 -6.001395 -3.135392 0.0000000 0.0000000
JUNB 18.795757 3.115301 0.0000000 0.0000000
SOCS3 15.948318 3.104679 0.0000000 0.0000000
PDGFA 4.698763 3.086656 0.0000026 0.0000128
MFAP5 -3.948243 -3.057630 0.0000787 0.0003336
LAMC2 8.059149 3.000062 0.0000000 0.0000000
MYBL2 3.614954 2.942651 0.0003004 0.0011921
CAV1 13.988802 2.941373 0.0000000 0.0000000
ITGA1 2.810849 2.935214 0.0049411 0.0177738
HLA-C 12.657085 2.924703 0.0000000 0.0000000
NFKBIA 19.223110 2.918888 0.0000000 0.0000000
STAT6 -11.588839 -2.894820 0.0000000 0.0000000
EGFR -7.535938 -2.870042 0.0000000 0.0000000
MAFB -5.609016 -2.814145 0.0000000 0.0000001
TEK 3.013768 2.803641 0.0025803 0.0096278
PIK3CG 4.427540 2.769206 0.0000095 0.0000441
CCND1 9.196863 2.637060 0.0000000 0.0000000
NFKB2 14.935277 2.614658 0.0000000 0.0000000
HDAC1 13.738701 2.609122 0.0000000 0.0000000
TNC -9.369732 -2.464361 0.0000000 0.0000000
NRP1 -8.410895 -2.451910 0.0000000 0.0000000
COL6A3 -4.339400 -2.429627 0.0000143 0.0000649
ERBB2 -4.713930 -2.420596 0.0000024 0.0000120
TP53 8.397938 2.414836 0.0000000 0.0000000
MMP2 -7.080902 -2.318094 0.0000000 0.0000000
ITGA5 17.589256 2.296214 0.0000000 0.0000000
BMP1 -16.530888 -2.227625 0.0000000 0.0000000
SMO -4.743149 -2.205583 0.0000021 0.0000105
BCL2L1 14.150189 2.178907 0.0000000 0.0000000
JAK1 14.034440 2.160701 0.0000000 0.0000000
IKBKB 11.276343 2.141437 0.0000000 0.0000000
AXIN2 -4.363968 -2.100143 0.0000128 0.0000586
WNT5A 7.458931 2.087795 0.0000000 0.0000000
ACKR3 10.054022 2.084263 0.0000000 0.0000000
STAT5A 9.193078 2.073626 0.0000000 0.0000000
MYC 9.197418 2.068635 0.0000000 0.0000000
IKZF2 -2.708779 -2.055110 0.0067531 0.0236124
PDGFRB -14.543082 -2.008962 0.0000000 0.0000000
BAX 9.147548 2.008727 0.0000000 0.0000000
TWIST1 -2.756824 -1.986752 0.0058366 0.0205513
MUC1 -3.746565 -1.956522 0.0001793 0.0007288
SOD2 6.608799 1.923183 0.0000000 0.0000000
ZAP70 -2.999130 -1.797797 0.0027075 0.0100278
VEGFA -9.500158 -1.790881 0.0000000 0.0000000
CXCL2 -3.120492 -1.790588 0.0018055 0.0068390
TAPBP 8.302095 1.776083 0.0000000 0.0000000
PREX2 2.873325 1.774583 0.0040618 0.0148239
NFKB1 5.656807 1.742856 0.0000000 0.0000001
TEAD4 4.895926 1.714321 0.0000010 0.0000050
KRAS 2.783078 1.694335 0.0053846 0.0190943
TAP1 2.491671 1.680091 0.0127144 0.0432462
EPHB3 -3.851426 -1.655681 0.0001174 0.0004853
RELA 10.722487 1.626555 0.0000000 0.0000000
CDKN1B 5.516062 1.610429 0.0000000 0.0000002
PKM 13.246241 1.581807 0.0000000 0.0000000
IL6R 2.637724 1.581026 0.0083465 0.0289807
TAP2 7.368522 1.567037 0.0000000 0.0000000
PDPN 7.741117 1.550819 0.0000000 0.0000000
CDK2 5.625519 1.535060 0.0000000 0.0000001
PPARD 6.258438 1.514070 0.0000000 0.0000000
MMP9 -3.326200 -1.511799 0.0008804 0.0034390
DUSP1 12.181810 1.468975 0.0000000 0.0000000
SERPINE1 4.660140 1.467474 0.0000032 0.0000152
HRAS 4.523263 1.372040 0.0000061 0.0000287
IDH1 3.203095 1.291888 0.0013596 0.0052292
CEBPB -4.449311 -1.268539 0.0000086 0.0000403
STING1 3.244730 1.256025 0.0011756 0.0045567
TGFBI -3.670541 -1.212372 0.0002420 0.0009760
DNMT3A 3.990792 1.168083 0.0000659 0.0002838
CDKN1A 7.622852 1.146154 0.0000000 0.0000000
DKK1 2.477612 1.089778 0.0132265 0.0446841
BAK1 3.646577 1.084874 0.0002658 0.0010630
IRF3 5.956850 1.067885 0.0000000 0.0000000
HIF1A 5.938131 1.038309 0.0000000 0.0000000
BRD4 8.365610 1.035384 0.0000000 0.0000000
IFNGR2 4.627274 1.022577 0.0000037 0.0000176
ARAF 2.803937 1.017162 0.0050483 0.0180296

5.5 Macrophage

names scores logfoldchanges pvals pvals_adj
FLT4 45.235348 17.898900 0.0000000 0.0000000
MMRN1 36.218163 10.236432 0.0000000 0.0000000
PROX1 35.871080 9.795492 0.0000000 0.0000000
C1QC -28.215542 -9.192366 0.0000000 0.0000000
CD163 -28.333025 -8.419353 0.0000000 0.0000000
HLA-DRA -30.139597 -7.539303 0.0000000 0.0000000
CSF1R -31.415611 -7.491040 0.0000000 0.0000000
COL1A1 -5.759960 -7.485166 0.0000000 0.0000000
CLDN5 30.179745 7.461066 0.0000000 0.0000000
EPHB4 34.964996 7.358389 0.0000000 0.0000000
CDH5 30.712711 7.234036 0.0000000 0.0000000
VWF 26.820099 7.225999 0.0000000 0.0000000
CIITA -19.404781 -7.100449 0.0000000 0.0000000
EPHA2 23.136395 6.853215 0.0000000 0.0000000
LRP5 27.142347 6.571948 0.0000000 0.0000000
ITGAX -15.929050 -6.460158 0.0000000 0.0000000
MAFB -27.114940 -6.438705 0.0000000 0.0000000
CSF3R -15.610359 -6.282949 0.0000000 0.0000000
ANGPT2 12.387028 6.176251 0.0000000 0.0000000
HLA-DMA -23.917181 -6.143620 0.0000000 0.0000000
HLA-DRB1 -10.033537 -5.890448 0.0000000 0.0000000
CD14 -21.893414 -5.725852 0.0000000 0.0000000
MMP9 -5.028206 -5.595316 0.0000005 0.0000023
FOS -20.502226 -5.592123 0.0000000 0.0000000
ITGB2 -19.111423 -5.338125 0.0000000 0.0000000
CYBB -10.570035 -5.325557 0.0000000 0.0000000
PECAM1 25.854963 5.232381 0.0000000 0.0000000
ETS1 26.233856 5.197754 0.0000000 0.0000000
TGFBR2 28.939135 5.175726 0.0000000 0.0000000
CD4 -13.724255 -5.072753 0.0000000 0.0000000
LRP1 -30.944944 -5.052610 0.0000000 0.0000000
NOTCH1 27.810156 5.049869 0.0000000 0.0000000
TREM2 -6.610495 -4.999965 0.0000000 0.0000000
ADAMTS4 10.373394 4.973886 0.0000000 0.0000000
CAV1 15.631512 4.888211 0.0000000 0.0000000
HLA-DPB1 -23.075144 -4.784143 0.0000000 0.0000000
CCL4 -2.767501 -4.735043 0.0056488 0.0179897
SIGLEC1 -11.690042 -4.723980 0.0000000 0.0000000
TLR2 -14.113093 -4.723290 0.0000000 0.0000000
WWTR1 25.468645 4.552478 0.0000000 0.0000000
CXCR4 -14.969394 -4.523808 0.0000000 0.0000000
SPP1 -4.185871 -4.413272 0.0000284 0.0001145
LAMC2 8.206511 4.365954 0.0000000 0.0000000
MARCO -4.973421 -4.320438 0.0000007 0.0000029
NOS3 3.796956 4.271498 0.0001465 0.0005507
COL4A1 23.807760 4.192233 0.0000000 0.0000000
SERPINE1 9.951945 4.153257 0.0000000 0.0000000
CSF2RA -7.880868 -4.142440 0.0000000 0.0000000
CCR1 -6.897551 -4.132929 0.0000000 0.0000000
FCGR3A -4.738967 -3.894251 0.0000021 0.0000094
MMRN2 5.685956 3.870323 0.0000000 0.0000001
PDCD1LG2 -2.413854 -3.748051 0.0157848 0.0472598
CEACAM1 3.603048 3.736437 0.0003145 0.0011648
ITGAM -14.335842 -3.729766 0.0000000 0.0000000
WNT5A 8.472052 3.718648 0.0000000 0.0000000
CCND1 9.734027 3.685252 0.0000000 0.0000000
KDR 15.288972 3.683546 0.0000000 0.0000000
CEBPB -19.162653 -3.623165 0.0000000 0.0000000
TEAD4 6.164411 3.616383 0.0000000 0.0000000
CMKLR1 -7.117741 -3.611054 0.0000000 0.0000000
LYZ -8.076860 -3.548180 0.0000000 0.0000000
PGF 7.924035 3.537687 0.0000000 0.0000000
PDPN 10.845285 3.459102 0.0000000 0.0000000
YAP1 20.174599 3.436991 0.0000000 0.0000000
MSR1 -3.328696 -3.375325 0.0008725 0.0030723
ITGA1 2.704030 3.360169 0.0068504 0.0216785
PDGFA 4.445983 3.351682 0.0000087 0.0000374
CD83 -6.491976 -3.301482 0.0000000 0.0000000
TMEM37 -7.656223 -3.296272 0.0000000 0.0000000
IL3RA 4.101983 3.283519 0.0000410 0.0001625
ITGA5 19.402636 3.225117 0.0000000 0.0000000
TGFBI -15.124540 -3.209434 0.0000000 0.0000000
STAT6 -13.408995 -3.198131 0.0000000 0.0000000
CD209 -3.280663 -3.110518 0.0010356 0.0035960
ACKR3 11.243085 3.092913 0.0000000 0.0000000
TGFBR3 9.676096 3.085863 0.0000000 0.0000000
KLF2 15.470725 2.957211 0.0000000 0.0000000
CXCL16 -9.046338 -2.900698 0.0000000 0.0000000
SOCS3 13.658674 2.894376 0.0000000 0.0000000
CCL2 5.729135 2.857231 0.0000000 0.0000000
FCGR2A -8.657062 -2.848609 0.0000000 0.0000000
NRP1 -10.372022 -2.817253 0.0000000 0.0000000
SERPINA1 -2.904340 -2.788966 0.0036803 0.0121062
HAVCR2 -9.028779 -2.744942 0.0000000 0.0000000
NCAM1 4.355743 2.679918 0.0000133 0.0000553
LAMP3 3.249776 2.664360 0.0011550 0.0039826
AMOTL2 4.530058 2.528394 0.0000059 0.0000254
IL2RA -3.296399 -2.524183 0.0009793 0.0034242
IL4I1 -3.603622 -2.406923 0.0003138 0.0011648
NEDD4 4.245523 2.398189 0.0000218 0.0000894
ICAM2 4.063209 2.357599 0.0000484 0.0001876
NFKB2 13.111306 2.356491 0.0000000 0.0000000
ELN 4.233717 2.322503 0.0000230 0.0000934
ENG 11.640049 2.316093 0.0000000 0.0000000
BST2 -6.191567 -2.281465 0.0000000 0.0000000
PDK4 -5.161625 -2.280601 0.0000002 0.0000011
CSF1 9.834950 2.263188 0.0000000 0.0000000
TP53 7.445043 2.259413 0.0000000 0.0000000
FN1 13.981584 2.215139 0.0000000 0.0000000
PREX2 2.836663 2.196042 0.0045588 0.0148979
IL6R -7.524688 -2.114200 0.0000000 0.0000000
CLEC14A 4.091924 2.104632 0.0000428 0.0001684
CCL3 -3.562489 -2.068161 0.0003674 0.0013506
HDAC1 10.795954 2.038043 0.0000000 0.0000000
PTK2 6.527106 2.033509 0.0000000 0.0000000
CXCL12 -2.563734 -2.023919 0.0103553 0.0321592
TEAD1 7.131980 1.988486 0.0000000 0.0000000
TCF7L2 9.194421 1.986073 0.0000000 0.0000000
PLVAP 5.882672 1.927855 0.0000000 0.0000000
SELPLG -3.013562 -1.914857 0.0025820 0.0085497
TGFB3 8.689459 1.873085 0.0000000 0.0000000
MRC1 -10.411856 -1.873005 0.0000000 0.0000000
CD40 -3.105374 -1.863478 0.0019004 0.0064639
CDK2 5.880513 1.863039 0.0000000 0.0000000
NFKBIA 11.091059 1.819244 0.0000000 0.0000000
ZEB1 5.570919 1.790472 0.0000000 0.0000001
FGFR1 10.516498 1.769329 0.0000000 0.0000000
JAK1 11.025790 1.740103 0.0000000 0.0000000
RELA 9.895500 1.687370 0.0000000 0.0000000
BAX 7.486488 1.686854 0.0000000 0.0000000
MYC 6.589891 1.679193 0.0000000 0.0000000
GPX3 -3.989517 -1.661514 0.0000662 0.0002546
LRP6 4.674272 1.616007 0.0000029 0.0000128
BCL2 -3.466184 -1.554042 0.0005279 0.0018854
JUNB 7.757832 1.512997 0.0000000 0.0000000
NFKB1 4.825512 1.510247 0.0000014 0.0000062
RGMB 2.653039 1.503856 0.0079771 0.0250852
SNAI2 2.790252 1.488276 0.0052667 0.0170143
LMNA 10.756605 1.463056 0.0000000 0.0000000
CTNNB1 10.486559 1.401059 0.0000000 0.0000000
DNMT3A 3.970185 1.341161 0.0000718 0.0002741
AKT3 2.787543 1.296738 0.0053109 0.0170222
ITGB1 6.575789 1.274869 0.0000000 0.0000000
PDGFB 5.912111 1.158092 0.0000000 0.0000000
TGFB1 8.081727 1.152926 0.0000000 0.0000000
BMP1 8.707891 1.142483 0.0000000 0.0000000
CDKN1A 5.481166 1.089727 0.0000000 0.0000002
IGF1R 3.088589 1.085979 0.0020111 0.0067486
HLA-C 6.401736 1.085662 0.0000000 0.0000000
HIF1A 5.404691 1.082416 0.0000001 0.0000003
ATF3 -4.339270 -1.053086 0.0000143 0.0000591
CDK4 4.977501 1.038995 0.0000006 0.0000029
BRD4 7.382982 1.032621 0.0000000 0.0000000
STING1 2.538962 1.031018 0.0111182 0.0343154
IRF3 5.111919 1.017732 0.0000003 0.0000015
VEGFA -2.517485 -1.017519 0.0118196 0.0362564
ICAM1 -4.115448 -1.008324 0.0000386 0.0001546

5.6 Mast cell

names scores logfoldchanges pvals pvals_adj
KIT -35.298214 -16.636616 0.0000000 0.0000000
FLT4 36.359356 16.574478 0.0000000 0.0000000
CTSG -30.450064 -15.565682 0.0000000 0.0000000
MMRN1 29.635664 12.993789 0.0000000 0.0000000
COL1A1 -8.256419 -11.849732 0.0000000 0.0000000
CLDN5 24.988739 11.118475 0.0000000 0.0000000
PROX1 29.075191 11.068053 0.0000000 0.0000000
PECAM1 29.081470 9.603505 0.0000000 0.0000000
CDH5 25.090961 8.516716 0.0000000 0.0000000
EPHA2 18.857985 8.189724 0.0000000 0.0000000
LAMC2 7.055347 8.168773 0.0000000 0.0000000
EPHB4 28.433023 7.951081 0.0000000 0.0000000
ANGPT2 10.145175 7.388753 0.0000000 0.0000000
VWF 21.658861 7.348731 0.0000000 0.0000000
CSF1 -19.900745 -6.572941 0.0000000 0.0000000
EGR1 -16.394962 -6.235933 0.0000000 0.0000000
THBD 14.970734 6.206938 0.0000000 0.0000000
PDGFB 12.762091 6.180831 0.0000000 0.0000000
COL4A1 20.734888 6.107423 0.0000000 0.0000000
MRC1 14.110034 6.046992 0.0000000 0.0000000
WWTR1 21.977097 5.950997 0.0000000 0.0000000
ETS1 21.800446 5.828736 0.0000000 0.0000000
PTGS2 -9.227437 -5.768790 0.0000000 0.0000000
LAMP3 3.069342 5.701388 0.0021453 0.0088649
CAV1 12.916644 5.630092 0.0000000 0.0000000
ADAMTS4 8.482302 5.575457 0.0000000 0.0000000
PGF 7.100119 5.526267 0.0000000 0.0000000
ITGAX -11.817466 -5.327488 0.0000000 0.0000000
KDR 13.554105 5.281285 0.0000000 0.0000000
WNT5A 7.221218 5.202876 0.0000000 0.0000000
TGFBR2 22.978678 5.094052 0.0000000 0.0000000
SOCS3 13.584214 4.997014 0.0000000 0.0000000
CCL2 5.956871 4.885377 0.0000000 0.0000000
SERPINE1 8.933406 4.824752 0.0000000 0.0000000
MMRN2 4.751090 4.804658 0.0000020 0.0000115
PDGFA 3.851649 4.724111 0.0001173 0.0005808
CXCR4 -8.036567 -4.503748 0.0000000 0.0000000
TEAD4 5.187738 4.488802 0.0000002 0.0000013
NOTCH1 21.415220 4.464276 0.0000000 0.0000000
ENG 12.987767 4.418426 0.0000000 0.0000000
CCND1 8.176953 4.360279 0.0000000 0.0000000
FN1 17.510372 4.263159 0.0000000 0.0000000
PDPN 9.306944 4.197070 0.0000000 0.0000000
IL3RA 3.533497 4.179955 0.0004101 0.0018308
ACKR3 10.195522 4.140923 0.0000000 0.0000000
KLF2 14.678189 4.060452 0.0000000 0.0000000
TGFBR3 8.419729 3.948400 0.0000000 0.0000000
TNFRSF9 -6.124310 -3.912399 0.0000000 0.0000000
ITGAM -13.269118 -3.880357 0.0000000 0.0000000
MYC 8.722062 3.834033 0.0000000 0.0000000
PTGDR2 -3.421651 -3.811966 0.0006224 0.0027299
CTSW -9.039966 -3.763929 0.0000000 0.0000000
LRP5 18.407625 3.663476 0.0000000 0.0000000
LRP6 5.229206 3.619845 0.0000002 0.0000010
SNAI2 3.329629 3.618145 0.0008696 0.0037240
YAP1 16.320122 3.549591 0.0000000 0.0000000
BST2 -10.985471 -3.531923 0.0000000 0.0000000
PREX2 2.678704 3.450054 0.0073908 0.0282090
STAT6 -12.808226 -3.436004 0.0000000 0.0000000
NCAM1 3.823316 3.394285 0.0001317 0.0006454
ZEB1 5.685184 3.381876 0.0000000 0.0000001
SOD2 6.872708 3.350679 0.0000000 0.0000000
ITGA4 -4.309857 -3.341032 0.0000163 0.0000888
ITGA5 15.698150 3.336625 0.0000000 0.0000000
CD22 -9.763500 -3.331090 0.0000000 0.0000000
KLRG1 -4.273181 -3.300256 0.0000193 0.0001036
TCF7L2 9.253540 3.284168 0.0000000 0.0000000
ACTA2 3.544690 3.276237 0.0003931 0.0017706
CEACAM1 2.784603 3.235635 0.0053593 0.0209349
ITGB2 -6.732074 -3.229836 0.0000000 0.0000000
NOS3 2.834166 3.228058 0.0045945 0.0180888
PLVAP 5.719176 3.216653 0.0000000 0.0000001
NFKBIA -12.050741 -3.073155 0.0000000 0.0000000
CD83 -3.642742 -3.064773 0.0002697 0.0012374
CD4 -3.350156 -3.004637 0.0008077 0.0035116
FGFR1 10.887585 2.881437 0.0000000 0.0000000
RET -4.715570 -2.791658 0.0000024 0.0000135
HAVCR2 -8.176788 -2.778566 0.0000000 0.0000000
VEGFA -10.672069 -2.764796 0.0000000 0.0000000
TEAD1 6.525067 2.693802 0.0000000 0.0000000
KRAS 2.514651 2.582281 0.0119150 0.0444590
ICAM1 -7.914353 -2.556723 0.0000000 0.0000000
JAK1 11.451610 2.555772 0.0000000 0.0000000
STAP1 -2.926353 -2.523744 0.0034296 0.0137185
CD274 -6.535888 -2.506416 0.0000000 0.0000000
HRAS 4.668775 2.486017 0.0000030 0.0000168
AMOTL2 3.697096 2.440707 0.0002181 0.0010287
CDK2 5.407839 2.386728 0.0000001 0.0000004
ICAM2 3.259498 2.386599 0.0011161 0.0047292
ITGB1 7.946404 2.322808 0.0000000 0.0000000
TP53 5.966288 2.285715 0.0000000 0.0000000
NEDD4 3.329051 2.283482 0.0008714 0.0037240
PKM 12.472107 2.246835 0.0000000 0.0000000
IGF1R 3.760701 2.175447 0.0001694 0.0008146
PRKCA -8.037517 -2.173464 0.0000000 0.0000000
LGALS9 7.498191 2.172484 0.0000000 0.0000000
HDAC1 8.930432 2.086977 0.0000000 0.0000000
TAP2 6.404836 2.071291 0.0000000 0.0000000
RGMB 2.508373 2.047264 0.0121288 0.0449216
BCL2L1 9.485123 1.996182 0.0000000 0.0000000
TGFB3 7.105447 1.994158 0.0000000 0.0000000
CXCL16 -3.996992 -1.988374 0.0000642 0.0003341
CDKN1A 7.006074 1.979546 0.0000000 0.0000000
BCL2 -3.885682 -1.942953 0.0001020 0.0005102
CTNNB1 10.754550 1.892763 0.0000000 0.0000000
CLEC14A 3.110685 1.857836 0.0018665 0.0077772
BAX 6.334085 1.810982 0.0000000 0.0000000
ICAM3 -3.912777 -1.745410 0.0000912 0.0004655
FOS -4.079101 -1.694183 0.0000452 0.0002405
IL6R -4.376891 -1.545817 0.0000120 0.0000661
HIF1A 5.532861 1.524770 0.0000000 0.0000002
SFRP2 -3.746824 -1.402247 0.0001791 0.0008528
LRP1 -3.044354 -1.334220 0.0023318 0.0094789
IKBKB 5.821358 1.327832 0.0000000 0.0000000
JUN 10.202998 1.286525 0.0000000 0.0000000
ELN 2.530098 1.274333 0.0114031 0.0428686
HDAC3 4.004055 1.262917 0.0000623 0.0003277
HLA-B 6.725424 1.253908 0.0000000 0.0000000
PIK3CG -3.974069 -1.229888 0.0000707 0.0003642
PTK2 3.603092 1.205447 0.0003145 0.0014293
INSR 3.060421 1.167134 0.0022103 0.0090585
NFE2L2 2.779482 1.167091 0.0054446 0.0211030
CD248 -2.757344 -1.154401 0.0058273 0.0224127
RAF1 3.899271 1.119336 0.0000965 0.0004873
RELA 5.117855 1.053447 0.0000003 0.0000018
BMP1 5.875339 1.039121 0.0000000 0.0000000

5.7 Smooth Muscle cell

names scores logfoldchanges pvals pvals_adj
COL1A1 -20.996437 -20.108192 0.0000000 0.0000000
FLT4 44.462265 15.825105 0.0000000 0.0000000
MMRN1 35.837070 10.416787 0.0000000 0.0000000
PROX1 35.494396 10.144096 0.0000000 0.0000000
ACTA2 -31.795290 -9.972496 0.0000000 0.0000000
PDGFRB -37.720340 -9.247806 0.0000000 0.0000000
PECAM1 30.463469 5.882178 0.0000000 0.0000000
MRC1 17.118620 5.854153 0.0000000 0.0000000
CLDN5 27.950174 5.604635 0.0000000 0.0000000
CDH5 28.512243 5.296866 0.0000000 0.0000000
EPHB4 31.256548 5.141222 0.0000000 0.0000000
CEACAM1 3.766085 5.077138 0.0001658 0.0009967
EGR1 -10.792938 -4.895118 0.0000000 0.0000000
TGFBR2 27.437937 4.830715 0.0000000 0.0000000
MYH11 -6.270687 -4.713664 0.0000000 0.0000000
LRP5 24.936739 4.677763 0.0000000 0.0000000
NDUFA4L2 -10.332066 -4.599361 0.0000000 0.0000000
VWF 23.343147 4.532220 0.0000000 0.0000000
SMOC2 -8.135152 -4.494476 0.0000000 0.0000000
PDPN 11.471095 4.412496 0.0000000 0.0000000
COL4A1 -17.562390 -4.385192 0.0000000 0.0000000
LAMC2 8.063821 4.111161 0.0000000 0.0000000
COL5A1 -23.727966 -4.083920 0.0000000 0.0000000
NRP1 -16.839422 -3.942974 0.0000000 0.0000000
CD248 -18.385832 -3.792705 0.0000000 0.0000000
FOS -11.640290 -3.736037 0.0000000 0.0000000
LGALS9 11.507880 3.348346 0.0000000 0.0000000
STAT6 -13.714140 -3.267770 0.0000000 0.0000000
LAMP3 3.352705 3.208935 0.0008003 0.0041680
EGFR -8.637122 -3.113345 0.0000000 0.0000000
CD40 -8.446769 -3.105172 0.0000000 0.0000000
NOTCH1 21.527735 3.081855 0.0000000 0.0000000
IRS1 -7.228665 -3.059417 0.0000000 0.0000000
KDR 14.056684 3.047568 0.0000000 0.0000000
DES -3.192075 -2.965473 0.0014125 0.0071341
SPRY2 -13.008330 -2.943933 0.0000000 0.0000000
IL3RA 3.878811 2.942234 0.0001050 0.0006561
WWTR1 19.731112 2.889727 0.0000000 0.0000000
FZD7 -3.168818 -2.884040 0.0015306 0.0076530
THBD 14.045283 2.882316 0.0000000 0.0000000
KLF2 15.251985 2.762932 0.0000000 0.0000000
CCL2 5.564962 2.746952 0.0000000 0.0000002
EPHA2 16.307700 2.736189 0.0000000 0.0000000
SOD2 6.975276 2.720080 0.0000000 0.0000000
LRP1 -15.634890 -2.674928 0.0000000 0.0000000
PTEN -2.753027 -2.615758 0.0059047 0.0265978
WNT5A 7.331167 2.516138 0.0000000 0.0000000
ERBB2 -4.674259 -2.508218 0.0000030 0.0000199
PDGFB 11.618394 2.499325 0.0000000 0.0000000
NFKBIA 14.544785 2.421089 0.0000000 0.0000000
NFKB2 12.676321 2.375955 0.0000000 0.0000000
ENG 11.604057 2.237547 0.0000000 0.0000000
ACKR3 9.326978 2.212598 0.0000000 0.0000000
TGFBR3 8.163472 2.208490 0.0000000 0.0000000
TNF -3.313707 -2.187430 0.0009207 0.0047458
CCND1 7.513607 2.139549 0.0000000 0.0000000
ITGA5 15.185333 2.095846 0.0000000 0.0000000
GPX3 -4.577629 -1.866199 0.0000047 0.0000305
NCAM1 4.008483 1.849094 0.0000611 0.0003917
TGFB1 12.541530 1.816917 0.0000000 0.0000000
TGFBI -6.331410 -1.752475 0.0000000 0.0000000
ANGPT2 6.140702 1.743900 0.0000000 0.0000000
STAT5A 7.410354 1.740503 0.0000000 0.0000000
ETS1 10.521313 1.638837 0.0000000 0.0000000
MMP11 -5.470502 -1.611378 0.0000000 0.0000003
VSIR 3.951943 1.574839 0.0000775 0.0004906
BST2 -2.792110 -1.526887 0.0052366 0.0240209
CEBPB -5.873260 -1.521937 0.0000000 0.0000000
JUN -3.659883 -1.513313 0.0002523 0.0014176
ICAM3 -3.429808 -1.509334 0.0006040 0.0032474
TNC -3.699632 -1.462015 0.0002159 0.0012268
BMP1 -8.920716 -1.445508 0.0000000 0.0000000
ITGA1 -4.600262 -1.439653 0.0000042 0.0000278
IKBKB 7.650526 1.426460 0.0000000 0.0000000
HDAC1 8.221089 1.412118 0.0000000 0.0000000
BCL2 -2.872716 -1.410375 0.0040696 0.0190168
ATF3 -7.065696 -1.379211 0.0000000 0.0000000
FGFR1 9.203445 1.348400 0.0000000 0.0000000
SOCS3 8.143292 1.323755 0.0000000 0.0000000
ELN 3.100267 1.314553 0.0019335 0.0095716
PGF -7.245413 -1.284468 0.0000000 0.0000000
PPARD 5.062893 1.271717 0.0000004 0.0000029
ICAM2 2.869468 1.235842 0.0041116 0.0190353
CTNNB1 9.429096 1.227940 0.0000000 0.0000000
ANGPT1 -3.763660 -1.208133 0.0001674 0.0009967
FN1 -3.740332 -1.197342 0.0001838 0.0010690
NFKB1 3.740204 1.125834 0.0001839 0.0010690
CDCA7 -2.772654 -1.112815 0.0055601 0.0252733
TP53 4.646734 1.094442 0.0000034 0.0000225
DNMT3A 3.411273 1.087610 0.0006466 0.0034394
HLA-C 5.967849 1.038034 0.0000000 0.0000000
PKM 7.479501 1.020708 0.0000000 0.0000000

5.8 T cell

names scores logfoldchanges pvals pvals_adj
EOMES -3.400761 -26.706500 0.0006720 0.0023661
COL1A1 -13.845674 -20.255121 0.0000000 0.0000000
FLT4 39.941800 15.124569 0.0000000 0.0000000
PROX1 32.140053 11.195617 0.0000000 0.0000000
MMRN1 32.203156 10.200131 0.0000000 0.0000000
CLDN5 27.363577 8.822340 0.0000000 0.0000000
CDH5 27.638943 8.167581 0.0000000 0.0000000
PECAM1 30.421830 7.601376 0.0000000 0.0000000
ANGPT2 11.222257 7.516079 0.0000000 0.0000000
VWF 23.926765 7.332612 0.0000000 0.0000000
CD3E -19.516031 -7.179794 0.0000000 0.0000000
EPHA2 20.668118 7.160447 0.0000000 0.0000000
EPHB4 30.812730 6.945785 0.0000000 0.0000000
FOXP3 -9.051171 -6.726066 0.0000000 0.0000000
CXCR4 -26.073612 -6.577494 0.0000000 0.0000000
THBD 16.527596 6.389972 0.0000000 0.0000000
TIGIT -5.847714 -6.204275 0.0000000 0.0000000
LRP5 23.805185 5.973184 0.0000000 0.0000000
TRAC -16.720135 -5.751883 0.0000000 0.0000000
GATA3 -12.049971 -5.700802 0.0000000 0.0000000
PRF1 -6.777646 -5.634010 0.0000000 0.0000000
MRC1 15.339237 5.598194 0.0000000 0.0000000
IL2RB -13.916772 -5.579718 0.0000000 0.0000000
CCR4 -12.722701 -5.472393 0.0000000 0.0000000
ITK -9.723122 -5.322735 0.0000000 0.0000000
ADAMTS4 9.315756 5.286111 0.0000000 0.0000000
CXCR6 -6.977539 -5.273532 0.0000000 0.0000000
CCL2 6.603717 5.227972 0.0000000 0.0000000
ITGB2 -18.406181 -5.209642 0.0000000 0.0000000
ZAP70 -18.958754 -5.144957 0.0000000 0.0000000
LAMC2 7.501861 5.068172 0.0000000 0.0000000
CCL4 -3.992447 -5.050675 0.0000654 0.0002658
CD27 -5.996791 -4.938039 0.0000000 0.0000000
TGFBR2 24.741720 4.926980 0.0000000 0.0000000
PTPRC -3.459183 -4.807740 0.0005418 0.0019490
CCL5 -8.399030 -4.794311 0.0000000 0.0000000
CD4 -9.029135 -4.750630 0.0000000 0.0000000
PDGFB 13.396407 4.735591 0.0000000 0.0000000
CD5 -15.327118 -4.724214 0.0000000 0.0000000
PDCD1 -9.330577 -4.529251 0.0000000 0.0000000
GZMH -3.672728 -4.509136 0.0002400 0.0009090
CD2 -11.901089 -4.499842 0.0000000 0.0000000
SERPINE1 9.754353 4.433006 0.0000000 0.0000000
CAV1 13.573511 4.429834 0.0000000 0.0000000
WWTR1 22.222220 4.377824 0.0000000 0.0000000
PGF 7.467175 4.373515 0.0000000 0.0000000
CD28 -5.212009 -4.355150 0.0000002 0.0000009
COL4A1 21.632513 4.332262 0.0000000 0.0000000
PDGFA 4.187020 4.297455 0.0000283 0.0001168
KLRK1 -5.870447 -4.260379 0.0000000 0.0000000
KDR 14.256578 4.241043 0.0000000 0.0000000
RORC -7.847099 -4.163980 0.0000000 0.0000000
CD3D -7.919256 -4.156508 0.0000000 0.0000000
MMRN2 5.120685 4.099026 0.0000003 0.0000014
ENG 13.992773 4.075697 0.0000000 0.0000000
PDPN 10.111738 4.059384 0.0000000 0.0000000
WNT5A 7.622160 3.960729 0.0000000 0.0000000
CEACAM1 3.249008 3.950698 0.0011581 0.0039660
SOCS3 13.949786 3.934454 0.0000000 0.0000000
CD40LG -3.432855 -3.909229 0.0005973 0.0021331
CTSW -8.130795 -3.879531 0.0000000 0.0000000
NKG7 -6.253910 -3.867290 0.0000000 0.0000000
NOS3 3.294531 3.827489 0.0009859 0.0034231
TRBC1 -6.809796 -3.822456 0.0000000 0.0000000
CCND1 8.748475 3.822440 0.0000000 0.0000000
NOTCH1 21.690516 3.747277 0.0000000 0.0000000
IKZF2 -5.749536 -3.611270 0.0000000 0.0000000
IRF4 -2.832867 -3.575692 0.0046133 0.0145989
ACKR3 10.647900 3.553622 0.0000000 0.0000000
TEAD4 5.442019 3.551893 0.0000001 0.0000003
GZMB -2.931268 -3.549000 0.0033758 0.0108199
ICAM3 -13.071366 -3.524682 0.0000000 0.0000000
IL2RA -4.566860 -3.475842 0.0000050 0.0000213
ITGA5 17.738049 3.461118 0.0000000 0.0000000
CTLA4 -5.093995 -3.373042 0.0000004 0.0000016
LAMP3 3.102048 3.320093 0.0019219 0.0063638
GZMA -3.791411 -3.313827 0.0001498 0.0005761
CIITA -2.681254 -3.296683 0.0073347 0.0227785
BCL2 -10.414518 -3.254471 0.0000000 0.0000000
STAT4 -4.120128 -3.167271 0.0000379 0.0001552
YAP1 17.361439 3.153681 0.0000000 0.0000000
LGALS9 10.130042 3.122557 0.0000000 0.0000000
DUSP1 17.836199 3.112409 0.0000000 0.0000000
IL3RA 3.564938 3.078259 0.0003639 0.0013479
CCR7 -4.610154 -3.039714 0.0000040 0.0000175
STAT6 -10.918195 -2.988075 0.0000000 0.0000000
TEK 2.512953 2.986847 0.0119725 0.0360618
SELPLG -5.341891 -2.788490 0.0000001 0.0000004
LRP6 5.384851 2.771006 0.0000001 0.0000003
CD8A -3.971329 -2.748166 0.0000715 0.0002859
JUN 14.815863 2.747525 0.0000000 0.0000000
ITGA4 -3.098482 -2.745725 0.0019451 0.0063985
CCR8 -2.753299 -2.718732 0.0058998 0.0185528
JUNB 12.440175 2.691635 0.0000000 0.0000000
FN1 15.273543 2.683996 0.0000000 0.0000000
TNFRSF18 -4.697996 -2.665153 0.0000026 0.0000117
PTK2 6.552845 2.610237 0.0000000 0.0000000
TCF7L2 9.409114 2.570765 0.0000000 0.0000000
TGFBR3 7.889864 2.562430 0.0000000 0.0000000
KLF2 12.568274 2.560196 0.0000000 0.0000000
INSR 5.647040 2.558333 0.0000000 0.0000001
CDKN1A 9.480101 2.527984 0.0000000 0.0000000
PREX2 2.711203 2.513145 0.0067040 0.0209499
CCR5 -2.481137 -2.456102 0.0130964 0.0392108
IGF1R 4.349052 2.363135 0.0000137 0.0000574
MYC 7.601710 2.346883 0.0000000 0.0000000
ETS1 -15.135080 -2.320390 0.0000000 0.0000000
IL6R -6.677629 -2.301140 0.0000000 0.0000000
TEAD1 6.684037 2.285530 0.0000000 0.0000000
LMNA 13.184059 2.238902 0.0000000 0.0000000
SOD2 5.666513 2.236107 0.0000000 0.0000001
FOS 6.030948 2.207432 0.0000000 0.0000000
PLVAP 5.629990 2.181190 0.0000000 0.0000001
NFKB2 11.456084 2.175959 0.0000000 0.0000000
HLA-DMA -2.524905 -2.171827 0.0115730 0.0350696
HLA-DRA -3.920986 -2.087061 0.0000882 0.0003472
TP53 6.250622 2.039009 0.0000000 0.0000000
BST2 -4.445169 -2.023512 0.0000088 0.0000375
NEDD4 3.524068 2.015537 0.0004250 0.0015398
SFRP2 -7.332056 -1.999527 0.0000000 0.0000000
COL5A1 -12.226352 -1.896043 0.0000000 0.0000000
IFNGR2 5.408309 1.890391 0.0000001 0.0000003
ELN 3.396526 1.860326 0.0006825 0.0023863
HIF1A 7.375879 1.859519 0.0000000 0.0000000
NFKBIA 9.996176 1.848740 0.0000000 0.0000000
XBP1 -3.972945 -1.844010 0.0000710 0.0002859
CLEC14A 3.235134 1.794262 0.0012159 0.0041356
AMOTL2 3.525099 1.791009 0.0004233 0.0015398
TBX21 -2.390760 -1.778680 0.0168135 0.0494516
CTNNB1 11.055628 1.710108 0.0000000 0.0000000
FGFR1 9.074462 1.664674 0.0000000 0.0000000
LRP1 -5.122969 -1.605921 0.0000003 0.0000014
RGMB 2.461969 1.583072 0.0138176 0.0411239
PIK3CG -5.857270 -1.539403 0.0000000 0.0000000
EGR1 7.329102 1.487095 0.0000000 0.0000000
CDKN1B -8.617757 -1.482979 0.0000000 0.0000000
CDK2 4.657265 1.464915 0.0000032 0.0000142
DNMT3A 3.761239 1.460846 0.0001691 0.0006453
BAX 6.261849 1.443502 0.0000000 0.0000000
HLA-DPB1 -3.831027 -1.436008 0.0001276 0.0004946
CDK4 5.518885 1.376419 0.0000000 0.0000002
BCL2L1 7.468234 1.334246 0.0000000 0.0000000
PPARD 4.653170 1.317327 0.0000033 0.0000143
CD276 4.346461 1.271443 0.0000138 0.0000576
NFE2L2 3.251349 1.267709 0.0011486 0.0039607
IDH1 2.563713 1.230789 0.0103559 0.0315729
ZEB1 3.944444 1.229542 0.0000800 0.0003174
HLA-B -9.211031 -1.189103 0.0000000 0.0000000
VEGFA 3.115532 1.179468 0.0018361 0.0061204
RELA 6.496903 1.167455 0.0000000 0.0000000
CD248 -3.545910 -1.155366 0.0003913 0.0014385
HDAC1 5.799210 1.091389 0.0000000 0.0000000
TGFB3 4.984450 1.063988 0.0000006 0.0000028
BMP1 8.492360 1.052245 0.0000000 0.0000000

6. Supplements

For original pictures and more details, please use the google drive link: ENT MERFISH Supplement